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Ruan Y, Cheng X, Zhang W, Zhao L, Xie J, Wen C, Li Y, Deng L, Huang L. [Mutation spectrum analysis of 23-site chip neonatal deafness genetic screening]. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2024; 38:267-272. [PMID: 38563166 DOI: 10.13201/j.issn.2096-7993.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Indexed: 04/04/2024]
Abstract
Objective:To analyze the mutation spectrum of 23-site chip newborn deafness genetic screening in Beijing, and to provide basis for genetic counseling and clinical diagnosis and treatment. Methods:The study included 21 006 babies born in Beijing from December 2022 to June 2023. All subjects underwent newborn deafness genetic screening in Beijing Tongren Hospital, covering 23 variants in 4 genes, the GJB2 gene(c.35delG, c.176_191del16, c.235delC, c.299_300delAT, c.109G>A, c.257C>G, c.512insAACG, c.427C>T, c.35insG), SLC26A4 gene(c.919-2A>G, c.2168A>G, c.1174A>T, c.1226G>A, c.1229C>T, c.1975G>C, c.2027T>A, c.589G>A, c.1707+5G>A, c.917insG, c.281C>T), Mt12SrRNA(m.1555A>G, m.1494C>T) and GJB3 gene(c.538C>T). The mutation detection rate and allele frequency were analyzed. Results:The overall mutation detection rate was 11.516%(2 419/21 006), with the GJB2 gene being the most frequently involved at 9.097%(1 911/21 006), followed by the SLC26A4 gene at 2.123%(446/21 006), the GJB3 gene at 0.362%(76/21 006) and Mt12SrRNA at 0.176%(37/21 006). Among the GJB2 genes, c.109G>A and c.235delC mutation detection rates were the highest, with 6.579%(1 382/21 006) and 1.795%(377/21 006), respectively. Of the SLC26A4 genes, c.919-2A>G and c.2168A>G had the highest mutation rates of 1.423%(299/21 006) and 0.233%(49/21 106), respectively. Regarding the allele frequency, GJB2 c.109G>A was the most common variant with an allele frequency of 3.359%(1 411/42 012), followed by the GJB2 c.235delC at 0.897%(377/42 012) and the SLC26A4 c.919-2A>G at 0.719%(302/42 012). Conclusion:23-site chip newborn deafness genetic screening in Beijing showed that GJB2 c.109G>A mutation detection rate and allele frequency were the highest. This study has enriched the epidemiological data of 23-site chip genetic screening mutation profiles for neonatal deafness, which can provide evidence for clinical practice.
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Affiliation(s)
- Yu Ruan
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Xiaohua Cheng
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Wei Zhang
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Liping Zhao
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Jinge Xie
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Cheng Wen
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Yue Li
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Lin Deng
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
| | - Lihui Huang
- Department of Otolaryngology Head and Neck Surgery,Beijing Tongren Hospital,Capital Medical University,Beijing Institute of Otolaryngology,Key Laboratory of Otolaryngology Head and Neck Surgery(Capital Medical University
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Glotov AS, Chernykh VB, Solovova OA, Polyakov AV, Donnikov MY, Kovalenko LV, Barbitoff YA, Nasykhova YA, Lazareva TE, Glotov OS. Russian Regional Differences in Allele Frequencies of CFTR Gene Variants: Genetic Monitoring of Infertile Couples. Genes (Basel) 2023; 15:45. [PMID: 38254935 PMCID: PMC10815393 DOI: 10.3390/genes15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
A male factor, commonly associated with poor semen quality, is revealed in about 50% of infertile couples. CFTR gene (Cystic Fibrosis Transmembrane Conduction Regulator) variants are one of the common genetic causes of azoospermia-related male infertility. Notably, the spectrum and frequency of pathogenic CFTR variants vary between populations and geographical regions. In this work, we made an attempt to evaluate the allele frequency (AF) of 12 common CFTR variants in infertile Russian men and healthy individuals from different districts of Russia. Because of the limited number of population-based studies on Russian individuals, we characterized the population AFs based on data from the Registry of Russian cystic fibrosis (CF) patients. In addition to the CF patient registry, we estimated the local frequencies of the same set of variants based on the results of genotyping of CF patients in local biocollections (from St. Petersburg and Yugra regions). AFs of common CFTR variants calculated based on registry and biocollection data showed good concordance with directly measured population AFs. The estimated region-specific frequencies of CFTR variants allowed us to uncover statistically significant regional differences in the frequencies of the F508del (c.1521_1523del; p.Phe508del) and CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb; p.Ser18ArgfsX) variants. The data from population-based studies confirmed previous observations that F508del, CFTRdele2,3(21kb), and L138ins (c.413_415dup; p.Leu138dup)variants are the most abundant among infertile patients, and their frequencies are significantly lower in healthy individuals and should be taken into account during genetic monitoring of the reproductive health of Russian individuals.
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Affiliation(s)
- Andrey S. Glotov
- D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia (Y.A.N.); (O.S.G.)
| | | | - Olga A. Solovova
- Research Centre for Medical Genetics, Moskvorechie Street 1, 115522 Moscow, Russia
| | | | - Maksim Yu. Donnikov
- Budgetary Institution of Highest Education of KHMAO-Yugra “Surgut State University”, 628400 Surgut, Russia; (M.Y.D.)
| | - Ludmila V. Kovalenko
- Budgetary Institution of Highest Education of KHMAO-Yugra “Surgut State University”, 628400 Surgut, Russia; (M.Y.D.)
| | - Yury A. Barbitoff
- D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia (Y.A.N.); (O.S.G.)
| | - Yulia A. Nasykhova
- D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia (Y.A.N.); (O.S.G.)
| | - Tatyana E. Lazareva
- D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia (Y.A.N.); (O.S.G.)
| | - Oleg S. Glotov
- D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia (Y.A.N.); (O.S.G.)
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Abdulhaleem M, Bandargal S, Pusztaszeri MP, Rajab M, Greenspoon H, Krasner JR, Da Silva SD, Forest VI, Payne RJ. The Impact of BRAF V600E Mutation Allele Frequency on the Histopathological Characteristics of Thyroid Cancer. Cancers (Basel) 2023; 16:113. [PMID: 38201541 PMCID: PMC10777954 DOI: 10.3390/cancers16010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND A BRAF V600E mutation in papillary thyroid cancer (PTC) has been shown to be associated with aggressive behavior. Nevertheless, not all BRAF V600E PTCs behave aggressively. Allele frequency (AF) is the number of mutated molecules divided by the total number of wild-type molecules at a specific location in the genome. The relationship between BRAF V600E AF and the histopathological features of thyroid malignancies is not well understood. We hypothesized that the BRAF V600E AF will correlate directly with aggressive histopathological behavior. The aim of this study was to examine this relationship. METHODS A retrospective chart review was performed for patients treated for BRAF V600E thyroid malignancies from 2019 to 2022 at McGill University tertiary care hospitals (n = 317). Patients with BRAF V600E-positive malignancies that included information on AF were included (n = 44). The correlation between AF and tumor histopathological features was analyzed. RESULTS Out of the 44 nodules with a BRAF V600E mutation, those with aggressive features of PTC had a mean AF of 25.8%, which was significantly higher than the non-aggressive group with a mean AF of 10.25% (p = 0.020). Additionally, there was a statistically significant difference in mean AF between patients with a positive sentinel LN (29%) and those with a negative sentinel LN (17.8%) (p = 0.021). Classical PTC was present in 29.5% (13/44) of nodules, with a mean AF of 15.6%. The tall cell subtype was found in 64% (28/44) of nodules, with a mean AF of 23%. Solid and hobnail subtypes were less common in this study, and there was no statistically significant relationship between AF and histopathological subtypes (p = 0.107). Nodules smaller than 1cm had a mean AF of 13.3%, while nodules ranging from 1 2cm had a mean AF of 20.6%, and those larger than 2cm had a mean AF of 27.7%. However, no statistical difference was observed between AF and nodule size (p = 0.160). CONCLUSION In this study, BRAF V600E mutations in conjunction with AF help to determine whether thyroid malignancies will display aggressive behavior. This pre-operative finding can help thyroid specialists to determine the extent of thyroidectomy and whether lymph node dissection is required.
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Affiliation(s)
- Mawaddah Abdulhaleem
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Royal Victoria Hospital, Montreal, QC H4A 3J1, Canada
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Saruchi Bandargal
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | | | - Mohannad Rajab
- Department of Otolaryngology—Head and Neck Surgery, King Faisal Specialist Hospital & Research Center, Al Madinah Al Munawwarah 42523, Saudi Arabia
| | - Hannah Greenspoon
- Faculty of Arts and Science, Queen’s University, Kingston, ON K7L 3N6, Canada
| | | | - Sabrina Daniela Da Silva
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Véronique-Isabelle Forest
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Royal Victoria Hospital, Montreal, QC H4A 3J1, Canada
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Richard J. Payne
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Royal Victoria Hospital, Montreal, QC H4A 3J1, Canada
- Department of Otolaryngology–Head and Neck Surgery, McGill University, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
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Moch J, Radtke M, Gburek-Augustat J, Karnstedt M, Schönnagel S, Drukewitz SH, Pilgram L, Hentschel J, Schumann I. Case report: Complete paternal isodisomy on chromosome 18 induces methylation changes in PARD6G-AS1 promotor in a case with arthrogryposis. Front Genet 2023; 14:1297754. [PMID: 38188501 PMCID: PMC10768175 DOI: 10.3389/fgene.2023.1297754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Uniparental disomy (UPD) is the inheritance of both alleles of a chromosome from only one parent. So far, the detection of UPDs in sequencing data is not well established and a known gap in next-generation sequencing (NGS) diagnostics. By developing a new tool for UPD detection, we re-evaluated an eight-year-old individual presenting with scoliosis, muscle weakness and global developmental delay. Previous panel analysis identified a homozygous likely pathogenic loss-of-function variant in the PIEZO2-gene associated with arthrogryposis (OMIM # 617146). Interestingly, during a re-evaluation process, we identified a region of homozygosity (ROH) covering over 95% of chromosome 18. Segregation and microsatellite analysis within the family revealed that only the father is a heterozygous carrier of the variant in PIEZO2 and confirmed paternal uniparental isodisomy (iUPD) on chromosome 18 in the individual. Further methylation analysis indicated demethylation of the promotor region of PARD6G-AS1, which is described to be maternally imprinted and could possibly influence the individuals' phenotype. Our report describes the first complete iUPD on chromosome 18 and highlights that UPDs can be a cause for homozygous pathogenic variants, which reduces the risk of reoccurrence in case of a new pregnancy in comparison to an autosomal recessive inheritance trait significantly.
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Affiliation(s)
- Johanna Moch
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Janina Gburek-Augustat
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University of Leipzig Medical Center, Leipzig, Germany
| | - Maike Karnstedt
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Senta Schönnagel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Stephan H. Drukewitz
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Laura Pilgram
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Isabell Schumann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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Khan R, De S, Dewangan R, Tamboli R, Gupta R. Potential status of A1 and A2 variants of bovine beta-casein gene in milk samples of Indian cattle breeds. Anim Biotechnol 2023; 34:4878-4884. [PMID: 37071545 DOI: 10.1080/10495398.2023.2200502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
This study aimed to determine the polymorphism in 7th exon of beta-casein gene (CSN2) gene in seven domestic (Kosali, Tharparkar, Gangatiri, Sahiwal, Gir, Khariar, Motu) and two exotic cattle breeds (Jersey and Holstein-Friesian). Genomic DNA was extracted from 1000 milk samples, and the C > A polymorphism in CSN2 was determined using the tetra-primer amplification refractory mutation system-polymerase chain reaction method. In all Indigenous cattle breeds, the mean frequency of A1A2 and A2A2 genotypes was 0.19 and 0.80, respectively. The A1A1 genotype was absent in all seven domestic cattle breeds. The frequency of the A2A2 genotype was highest in the Gir breed (0.93). However, the Sahiwal, Tharparkar, and Motu breeds also had a higher frequency of A2A2 genotype compared to other breeds. In contrast, Gangatiri breed of India showed lowest frequency of A2A2 genotype. The mean A1 and A2 allele frequency was 0.09 and 0.91, respectively. In exotic breeds, the mean frequencies of the A1A1, A1A2, and A2A2 genotypes were 0.42, 0.55, and 0.03, respectively. Similarly, the mean A1 and A2 allele frequency was 0.69 and 0.31, respectively. This study suggests the high potential of Gir, Sahiwal, Tharparkar, and Motu cattle for A2 milk production since they carry a favorable A2 genotype.
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Affiliation(s)
- Rupali Khan
- Parul Institute of Applied Sciences, Parul University, Vadodara, India
| | - Sachinandan De
- Animal Biotechnology Center, National Dairy Research Institute, Karnal, India
| | | | | | - Reeshu Gupta
- Parul Institute of Applied Sciences, Parul University, Vadodara, India
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Vlasenko NV, Chanyshev MD, Dubodelov DV, Serkov AA, Solopova GG, Sacuk AV, Snicar AV, Semenenko TА, Kuzin SN, Akimkin VG. Distribution of human gene polymorphisms allele frequencies associated with viral infections. Vopr Virusol 2023; 68:404-414. [PMID: 38156574 DOI: 10.36233/0507-4088-189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION The design of studies aimed at finding the association between the genetic factor and the studied feature (disease) involves a comparison of the ratio of genotypes or allelic proportions in the study group with those in the control group. At the stage of determining the ratio of genotypes of the studied polymorphisms in the reference group, researchers meet a number of problems, which are the subject of the present work. Aim of the work is to provide scientific rationale for the feasibility of creating a national information system comprising genetic data of the relatively healthy population of Russia, incorporating its ethnic diversity. MATERIALS AND METHODS The study group, total 1020 people, was genotyped for a number of single nucleotide polymorphisms of human genes. A comparative characteristic of the frequency distribution of the studied polymorphisms with those presented in international databases as reference data was carried out using χ2 index. RESULTS The frequency of SNP rs4986790 of the TLR4 gene significantly differs from the EUR population (p = 0.032) and the CEU subpopulation (p = 0.047). The allele frequencies of the rs1800795 (IL6) and rs1800896 (IL10) polymorphisms in the study population differ from the CEU subgroup (p = 0.030 and 0.012, respectively). The frequency of SNP rs2295119 (HLA-DPA2) in the study group is significantly different from the EUR population (p = 0.034). CONCLUSION The analysis carried out in this work confirms the need to create a domestic information system containing data on the occurrence of SNP alleles and genotypes for a conditionally healthy population and in subgroups with various pathological conditions.
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Affiliation(s)
- N V Vlasenko
- Central Research Institute for Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - M D Chanyshev
- Central Research Institute of Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - D V Dubodelov
- Central Research Institute for Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - A A Serkov
- Central Research Institute for Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - G G Solopova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology
| | - A V Sacuk
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology
| | | | - T А Semenenko
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology
| | - S N Kuzin
- Central Research Institute for Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
| | - V G Akimkin
- Central Research Institute for Epidemiology, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
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Gunsel AS, Ergoren MC, Kemal H, Kafshboran HR, Cerit L, Turgay A, Duygu H. Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population. Genes (Basel) 2023; 14:1967. [PMID: 37895316 PMCID: PMC10606490 DOI: 10.3390/genes14101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions.
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Affiliation(s)
- Aziz Suat Gunsel
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus;
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hatice Kemal
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | | | - Levent Cerit
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Ayla Turgay
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hamza Duygu
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
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Esdaile E, Knickelbein KE, Donnelly CG, Ferneding M, Motta MJ, Story BD, Avila F, Finno CJ, Gilger BC, Sandmeyer L, Thomasy S, Bellone RR. Additional evidence supports GRM6 p.Thr178Met as a cause of congenital stationary night blindness in three horse breeds. Vet Ophthalmol 2023. [PMID: 37815029 DOI: 10.1111/vop.13151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Congenital stationary night blindness (CSNB) is an ocular disorder characterized by nyctalopia. An autosomal recessive missense mutation in glutamate metabotropic receptor 6 (GRM6 c.533C>T, p.(Thr178Met)), called CSNB2, was previously identified in one Tennessee Walking Horse and predicted to reduce binding affinity of the neurotransmitter glutamate, impacting the retinal rod ON-bipolar cell signaling pathway. Thus, the first aim was to identify the allele frequency (AF) of CSNB2 in breeds with reported cases of CSNB and breeds closely related to the Tennessee Walking Horse. The second aim was to perform ocular examinations in multiple breeds to confirm the link between genotype and CSNB phenotype. In evaluating 3518 horses from 14 breeds, the CSNB2 allele was identified in nine previously unreported breeds. The estimated AF was highest in pacing Standardbreds (0.17) and lowest in American Quarter Horses (0.0010). Complete ophthalmic examinations and electroretinograms (ERG) were performed on 19 horses from three breeds, including one CSNB2 homozygote from each breed. All three CSNB2/CSNB2 horses had an electronegative ERG waveform under scotopic light conditions consistent with CSNB. The remaining 16 horses (seven CSNB2/N and nine N/N) had normal scotopic ERG results. All horses had normal photopic ERGs. This study provides additional evidence that GRM6 c.533C>T homozygosity is likely causal to CSNB in Tennessee Walking Horses, Standardbreds, and Missouri Fox Trotting Horses. Genetic testing is recommended for breeds with the CSNB2 allele to limit the production of affected horses. This study represents the largest across-breed identification of CSNB in the horse and suggests that this disorder is likely underdiagnosed.
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Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Kelly E Knickelbein
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Callum G Donnelly
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Michelle Ferneding
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Monica J Motta
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Brett D Story
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Brian C Gilger
- Department of Clinical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Department of Ophthalmology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sara Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Department of Ophthalmology & Vision Science, School of Medicine, University of California, Davis, Sacramento, California, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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9
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Wu M, Yavuzyiğitoğlu S, Brosens E, Ramdas WD, Kiliç E. Worldwide Incidence of Ocular Melanoma and Correlation With Pigmentation-Related Risk Factors. Invest Ophthalmol Vis Sci 2023; 64:45. [PMID: 37902747 PMCID: PMC10617638 DOI: 10.1167/iovs.64.13.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023] Open
Abstract
Purpose The worldwide incidence of ocular melanoma (OM), uveal melanoma (UM), and conjunctival melanoma has last been reported on 15 years ago. Recently, light iris color and four specific single-nucleotide-polymorphisms (SNPs) have been identified as a UM-risk factor. Furthermore, six iris color predicting SNPs have been discovered (IrisPlex). Interestingly, two of these (rs129138329 and rs12203592) are also UM-risk factors. We collected worldwide incidence data of OM and investigated its correlations with iris color, IrisPlex SNPs, and UM-risk SNPs. Methods Cases of OM, as defined by the International Classification of Diseases Oncology C69 (eye), 8720/3 to 8790/3 (malignant melanoma), and 8000 to 8005 (malignant neoplasm), between 1988 and 2012, were extracted from the Cancer Incidence in Five Continents. Incidence rates were age-standardized and their trends were analyzed with joinpoint regression and age period cohort modeling. Frequencies for each country of iris color, IrisPlex SNPs, and UM-risk SNPs were collected from the literature. Results Incidence rates were generally ≥8.0 cases per million person-years in Northern Europe, Western Europe, and Oceania; 2.0 to 7.9 in North America, Eastern Europe, and Southern Europe; and <2.0 in South America, Asia, and Africa. OM incidence correlated with latitude (r = 0.77, P ≤ 0.001) and is expressed as a north-to-south decreasing gradient in Europe. SNP rs12913832 correlated with OM incidence (r = 0.83, P ≤ 0.001), blue iris color (r = 0.56, P ≤ 0.05), green iris color (r = 0.51, P ≤ 0.05), and brown iris color (r = -0.64, P ≤ 0.01). Trends were stable for most countries (28/35). Conclusions OM incidence is highest in populations of European ancestry and lowest in populations of Asian and African ancestry. Overall, trends are stable, and the spatial correlation among OM incidence, iris color, and rs12913832 may support the role of pigmentation-related risk factors in OM development.
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Affiliation(s)
- Mike Wu
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Serdar Yavuzyiğitoğlu
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Wishal D. Ramdas
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - on behalf of the Rotterdam Ocular Melanoma Study Group (ROMS)
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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10
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Yi S, Qin Z, Zhou X, Chen J, Yi S, Chen Q, Huang L, Zhang Q, Chen B, Luo J. Early onset horizontal gaze palsy and progressive scoliosis due to a noncanonical splicing-site variant and a missense variant in the ROBO3 gene. Mol Genet Genomic Med 2023; 11:e2215. [PMID: 37330975 PMCID: PMC10496041 DOI: 10.1002/mgg3.2215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Homozygous or compound heterozygous ROBO3 gene mutations cause horizontal gaze palsy with progressive scoliosis (HGPPS). This is an autosomal recessive disorder that is characterized by congenital absence or severe restriction of horizontal gaze and progressive scoliosis. To date, almost 100 patients with HGPPS have been reported and 55 ROBO3 mutations have been identified. METHODS We described an HGPPS patient and performed whole-exome sequencing (WES) to identify the causative gene. RESULTS We identified a missense variant and a splice-site variant in the ROBO3 gene in the proband. Sanger sequencing of cDNA revealed the presence of an aberrant transcript with retention of 700 bp from intron 17, which was caused by a variation in the noncanonical splicing site. We identified five additional ROBO3 variants, which were likely pathogenic, and estimated the overall allele frequency in the southern Chinese population to be 9.44 × 10-4 , by a review of our in-house database. CONCLUSION This study has broadened the mutation spectrum of the ROBO3 gene and has expanded our knowledge of variants in noncanonical splicing sites. The results could help to provide more accurate genetic counseling to affected families and prospective couples. We suggest that the ROBO3 gene should be included in the local screening strategy.
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Affiliation(s)
- Sheng Yi
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Zailong Qin
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Xunzhao Zhou
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Junjie Chen
- Department of RadiologyMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Shang Yi
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Qiuli Chen
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Limei Huang
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Qinle Zhang
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Biyan Chen
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Jingsi Luo
- Genetic and Metabolic Central LaboratoryGuangxi Birth Defects Research and Prevention Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric DiseasesGuangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
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Iancu Loga LI, Dican L, Chiorean AD, Chelaru VF, Elec FI, Catana CS, Marta MM, Lucaciu RL, Hangan AC, Bondor CI, Vica ML, Matei HV. Association between Human Leukocyte Antigen and End-Stage Renal Disease in Patients from Transylvania, Romania. Int J Mol Sci 2023; 24:13383. [PMID: 37686189 PMCID: PMC10488296 DOI: 10.3390/ijms241713383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
End-stage renal disease (ESRD) is the final stage of chronic kidney disease. This study explored the association between human leukocyte antigen (HLA) and ESRD. The interaction between genetic and environmental factors may also play a role in the development of ESRD. The study included 2392 ESRD patients who were awaiting renal transplantation. Blood samples were genotyped by SSOP and SSP-PCR methods. Multivariate logistic regression analysis showed that HLA-A*11 (p = 0.027), HLA-A*34 (p = 0.017), HLA-A*69 (p = 0.012), HLA-B*41 (p < 0.001), HLA-B*50 (p = 0.004), HLA-DRB1*10 (p = 0.027), and HLA-DRB1*14 (p = 0.004) were positively associated with ESRD (OR > 1); HLA-DRB1*07 (p < 0.001), HLA-DRB1*08 (p = 0.005), and HLA-DRB1*13 (p < 0.001) were protective against ESRD (OR < 1); and the three-locus haplotype HLA-A*02-B*41-DRB1*03, containing one susceptible allele, was strongly associated with ESRD (p < 0.001, OR = 3.15). In conclusion, this retrospective analysis of HLA typing in patients with ESRD of various etiologies suggests that molecular data on the HLA polymorphism should be collected in order to identify high-risk ESRD patients and to improve graft survival after kidney transplantation.
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Affiliation(s)
- Luminita-Ioana Iancu Loga
- Department of Cellular and Molecular Biology, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (L.-I.I.L.); (A.D.C.); (M.L.V.); (H.V.M.)
- Clinical Institute of Urology and Renal Transplantation, 400000 Cluj-Napoca, Romania;
| | - Lucia Dican
- Clinical Institute of Urology and Renal Transplantation, 400000 Cluj-Napoca, Romania;
- Department of Medical Biochemistry, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Alin Dan Chiorean
- Department of Cellular and Molecular Biology, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (L.-I.I.L.); (A.D.C.); (M.L.V.); (H.V.M.)
| | - Vlad Florin Chelaru
- Department of Medical Education, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.F.C.); (M.M.M.)
| | - Florin Ioan Elec
- Clinical Institute of Urology and Renal Transplantation, 400000 Cluj-Napoca, Romania;
- Department of Urology, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Cristina Sorina Catana
- Department of Medical Biochemistry, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Monica Mihaela Marta
- Department of Medical Education, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.F.C.); (M.M.M.)
| | - Roxana Liana Lucaciu
- Department of Pharmaceutical Biochemistry and Clinical Laboratory, Faculty of Pharmacy, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Adriana Corina Hangan
- Department of Inorganic Chemistry, Faculty of Pharmacy, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Cosmina Ioana Bondor
- Department of Medical Informatics and Biostatistics, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Mihaela Laura Vica
- Department of Cellular and Molecular Biology, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (L.-I.I.L.); (A.D.C.); (M.L.V.); (H.V.M.)
| | - Horea Vladi Matei
- Department of Cellular and Molecular Biology, Faculty of Medicine, “Iuliu-Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (L.-I.I.L.); (A.D.C.); (M.L.V.); (H.V.M.)
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Lakoš Jukić I, Mokos M, Marinović B. HLA class II antigens in Croatian patients with pemphigus vulgaris and their correlation with anti-desmoglein antibodies. Front Immunol 2023; 14:1200992. [PMID: 37529044 PMCID: PMC10387520 DOI: 10.3389/fimmu.2023.1200992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Pemphigus vulgaris (PV) is an acquired autoimmune blistering disease characterized by the production of autoantibodies targeting desmosomal cadherins, primarily desmoglein 1 and desmoglein 3, leading to acantholysis. The etiology of PV is multifactorial, including genetic susceptibility. This retrospective study aimed to evaluate the association of HLA class II alleles and PV and to examine the impact of PV-associated HLA class II alleles on the concentration of anti-desmoglein antibodies. The study group included 30 patients in whom the diagnosis of PV was confirmed by histopathological analysis, immunofluorescence findings, and ELISA testing for detecting antibodies against desmoglein 1 and desmoglein 3. HLA class II alleles were typed by polymerase chain reaction with sequence-specific primers (PCR-SSP). The control group consisted of 190 healthy volunteer blood donors. Data analysis revealed a significantly higher frequency of HLA class II alleles in our population of patients with PV, including HLA-DRB1*04:02, HLA-DRB1*14:54, HLA-DQB1*03:02, HLA-DQB1*05:03, HLA- DQA1*03:01, and HLA-DQA1*01:04, as well as a significantly lower frequency of HLA-DQA1*05:01 compared to the control group. We have also investigated the influence of risk alleles for PV, recognized in almost all study populations, HLA-DRB1*04:02 and HLA-DQB1*05:03, on the concentration of antibodies against desmogleins 1 and 3 in relation to the presence of these alleles. The results showed significantly higher levels of antibodies directed against desmoglein 3 among patients with DRB1*04:02 compared to patients without this allele. No difference was found for anti-desmoglein 1 antibodies. Regarding DQB1*05:03 allele, statistical analysis showed no differences in the concentration of anti-desmoglein antibodies in patients carrying this allele versus those without it.
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Affiliation(s)
- Ines Lakoš Jukić
- Department of Dermatovenereology, University Hospital Centre Zagreb, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Mislav Mokos
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Branka Marinović
- Department of Dermatovenereology, University Hospital Centre Zagreb, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
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13
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Jung K, Kim JG, Shin S, Roh EY, Hong YJ, Song EY. Allele and haplotype frequencies of 11 HLA loci in Koreans by next-generation sequencing. HLA 2023; 101:602-612. [PMID: 36719349 DOI: 10.1111/tan.14980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 12/24/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Data on HLA genotype distribution, including DQA1 and DPA1, in the Korean population are limited. We aimed to investigate the allele and haplotype frequencies of 11 HLA loci in 339 Korean subjects using next-generation sequencing (NGS)-based HLA typing. A total of 339 samples from unrelated healthy subjects were genotyped for HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1, -DQA1, -DPB1, and -DPA1 using two different NGS-based HLA typing kits (166 tested using the NGSgo-MX11-3 kit [GenDx, Netherlands] and 173 by the AllType NGS 11 Loci Amplification kit [One Lambda, USA]). PyPop software was used to estimate allele and haplotype frequencies and linkage disequilibrium between the loci. Additionally, a principal component analysis was performed to compare the allele distribution of Koreans with that of other populations. A total of 214 HLA alleles (97 class I and 117 class II alleles) were assigned. The most frequent alleles for each locus were A*24:02:01 (24.78%), B*15:01:01 (10.18%), C*01:02:01 (18.44%), DRB1*04:05:01 (9.59%), DRB3*02:02:01 (13.72%), DRB4*01:03:01 (25.81%), DRB5*01:01:01 (9.0%), DQA1*01:02:01 (16.96%), DQB1*03:01:01 (14.31%), DPA1*01:03:01 (44.4%), and DPB1*05:01:01 (35.1%), respectively. The most frequent haplotypes were A*33:03:01-C*03:02:02-B*58:01:01 for HLA class I (5.01%) and DRB1*04:05:01-DQA1*03:03:01-DQB1*04:01:01-DPA1*02:02:02-DPB1*05:01:01 for HLA class II (6.23%). The total allelic ambiguities by NGS were estimated to be minimal and considerably decreased compared with those by Sanger sequencing. The Japanese population had the most similar allele distribution to Koreans, followed by the Chinese population. Frequency data of 11 HLA loci in Koreans can provide essential data for population genetics and disease association studies.
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Affiliation(s)
- Kiwook Jung
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Jisoo G Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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Hernández AI, Specht CD. Putative adaptive loci show parallel clinal variation in a California-endemic wildflower. Mol Ecol 2023. [PMID: 37246603 DOI: 10.1111/mec.17029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/30/2023]
Abstract
As the global climate crisis continues, predictions concerning how wild populations will respond to changing climate conditions are informed by an understanding of how populations have responded and/or adapted to climate variables in the past. Changes in the local biotic and abiotic environment can drive differences in phenology, physiology, morphology and demography between populations leading to local adaptation, yet the molecular basis of adaptive evolution in wild non-model organisms is poorly understood. We leverage comparisons between two lineages of Calochortus venustus occurring along parallel transects that allow us to identify loci under selection and measure clinal variation in allele frequencies as evidence of population-specific responses to selection along climatic gradients. We identify targets of selection by distinguishing loci that are outliers to population structure and by using genotype-environment associations across transects to detect loci under selection from each of nine climatic variables. Despite gene flow between individuals of different floral phenotypes and between populations, we find evidence of ecological specialization at the molecular level, including genes associated with key plant functions linked to plant adaptation to California's Mediterranean climate. Single-nucleotide polymorphisms (SNPs) present in both transects show similar trends in allelic similarity across latitudes indicating parallel adaptation to northern climates. Comparisons between eastern and western populations across latitudes indicate divergent genetic evolution between transects, suggesting local adaptation to either coastal or inland habitats. Our study is among the first to show repeated allelic variation across climatic clines in a non-model organism.
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Affiliation(s)
- Adriana I Hernández
- School of Integrative Plant Science, Section of Plant Biology and The L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
| | - Chelsea D Specht
- School of Integrative Plant Science, Section of Plant Biology and The L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
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15
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Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Vatsyayan A, Jolly B, Sivasubbu S, Scaria V. Genetic landscape of human platelet antigen variants in the Indian population analysed from 1029 whole genomes. Int J Immunogenet 2023; 50:134-143. [PMID: 37160415 DOI: 10.1111/iji.12622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Genetic variants in human platelet antigens (HPAs) considered allo- or auto antigens are associated with various disorders, including neonatal alloimmune thrombocytopenia, platelet transfusion refractoriness and post-transfusion purpura. Although global differences in genotype frequencies were observed, the distributions of HPA variants in the Indian population are largely unknown. This study aims to explore the landscape of HPA variants in India to provide a basis for risk assessment and management of related complications. Population-specific frequencies of genetic variants associated with the 35 classes of HPAs (HPA-1 to HPA-35) were estimated by systematically analysing genomic variations of 1029 healthy Indian individuals as well as from global population genome datasets. Allele frequencies of the most clinically relevant HPA systems in the Indian population were found as follows, HPA-1a - 0.884, HPA-1b - 0.117, HPA-2a - 0.941, HPA-2b - 0.059, HPA-3a - 0.653, HPA-3b - 0.347, HPA-4a - 0.999, HPA-4b - 0.0010, HPA-5a - 0.923, HPA-5b - 0.077, HPA-6a - 0.998, HPA-6b - 0.002, HPA-15a - 0.582 and HPA-15b - 0.418. This study provides the first comprehensive analysis of HPA allele and genotype frequencies using large scale representative whole genome sequencing data of the Indian population.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aastha Vatsyayan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Badrachalam R, Mani V, Kumar R, Shafiulla A. Vitamin D receptor (BsmI) gene polymorphism and allele frequency among chronic kidney disease patients in south Indian population. Bioinformation 2023; 19:380-384. [PMID: 37822821 PMCID: PMC10563556 DOI: 10.6026/97320630019380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
The vitamin D receptor (VDR) axis plays an important role in multiple physiological renal functions. BsmI gene is one among the VDR gene plays a vital role in maintaining this VDR axis and any polymorphism in VDR gene will cause dysfunction of renal tissues. The main objective of the study is to study the link between BsmI VDR gene polymorphism and Chronic Kidney Disease (CKD). This was a case-control study, which includes 100 cases and 100 controls. BsmI gene analysis was done by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP). Among 100 CKD study participants, BB (wild-type) genotype of BsmI gene was present in 7 patients (7%), Bb (heterozygous) genotype was present in 23 patients (23%) and bb (mutant) genotype was present in 70 patients (70%). And among 100 controls, 92 subjects were found to have BB genotype and 8 subjects were found to have Bb genotype and none of subjects were found to have bb genotypes. CKD patients with Bb and bb genotypes were found to have significantly elevated serum urea, creatinine and decreased Glomerular Filtration Rate (GFR) when compared to the BB genotype of BsmI gene. 'b' allele of BsmI gene, Bb and bb genotypes of BsmI gene plays a greater role in Guanine/Adenine single nucleotide polymorphism of BsmI gene in CKD.
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Affiliation(s)
- Ramya Badrachalam
- Department of Biochemistry, Sri Manakula Vinayagar Medical College and Hospital, Puducherry - 605107, Tamil Nadu, India
| | - Vadivel Mani
- Department of Biochemistry, Konaseema Institute of Medical sciences and research foundation, Amalapuram, East Godavari Dt-533201, Andhra Pradesh, India
| | - Ravi Kumar
- Department of Biochemistry, Sri Manakula Vinayagar Medical College and Hospital, Puducherry - 605107, Tamil Nadu, India
| | - Asmathulla Shafiulla
- Department of Biochemistry, All India Institute of Medical Sciences, Madurai- 625006, Tamilnadu, India
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17
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Santiago-González JC, Kerns DL, Head GP, Yang F. A Modified F2 Screen for Estimating Cry1Ac and Cry2Ab Resistance Allele Frequencies in Helicoverpa zea (Lepidoptera: Noctuidae). J Econ Entomol 2023; 116:289-296. [PMID: 36610074 DOI: 10.1093/jee/toac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 05/30/2023]
Abstract
Evaluating the frequency of resistance alleles is important for resistance management and sustainable use of transgenic crops that produce insecticidal proteins from Bacillus thuringiensis. Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) is a major crop pest in the United States that has evolved practical resistance to the crystalline (Cry) proteins in Bt corn and cotton. The standard F2 screen for estimating resistance allele frequency does not work well for H. zea because successful single-pair matings are rare. In this study, we developed and implemented a modified F2 screen for H. zea that generates F1 progeny by crossing three laboratory susceptible female moths with one feral male moth instead of single-pair crosses. During 2019-2020, we used this modified method to establish 192 F2 families from 623 matings between susceptible females and feral males from Arkansas, Louisiana, Mississippi, and Tennessee. From each F2 family, we screened 128 neonates against discriminating concentrations of Cry1Ac and Cry2Ab in diet overlay bioassays. Based on these discriminating concentration bioassays, families were considered positive for resistance if at least five larvae survived to second instar, including at least one to third instar. The percentage of positive families was 92.7% for Cry1Ac and 38.5% for Cry2Ab, which yields an estimated resistance allele frequency (with 95% confidence interval) of 0.722 (0.688-0.764) for Cry1Ac and 0.217 (0.179-0.261) for Cry2Ab. The modified F2 screen developed and implemented here may be useful for future resistance monitoring studies of H. zea and other pests.
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Affiliation(s)
| | - David L Kerns
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | | | - Fei Yang
- Department of Entomology, Texas A&M University, College Station, TX, USA
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18
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Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Jolly B, Sivasubbu S, Scaria V. Genetic landscape of human neutrophil antigen variants in India from population-scale genomes. HLA 2023; 101:262-269. [PMID: 36502377 DOI: 10.1111/tan.14938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Antibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia, transfusion-related acute lung injury, and other nonhemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. Ten genetic variants in four human genes encoding alleles of HNAs class I-V approved by the International Society of Blood Transfusion-Granulocyte Immunobiology Working Party were used in the analysis. Genetic variants from whole genome sequences of 1029 healthy Indian individuals corresponding to HNA alleles were analyzed. The frequencies of the variants were compared with global population datasets using an in-house computational pipeline. In HNA class I, allele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 encoding HNA-1a, HNA-1b, and HNA-1c were 0.07, 0.8, and 0.13, respectively. HNA class 3 alleles namely SLC44A2*01 (encoding HNA-3a) and SLC44A2*02 (encoding HNA-3b) were found at allele frequencies of 0.78 and 0.22, respectively. The frequencies of ITGAM*01 encoding HNA-4a and ITGAM*02 encoding HNA-4a were 0.95 and 0.05, respectively. Furthermore, allele frequencies of HNA class 5 alleles were 0.32 for ITGAL*01 (encoding HNA-5a) and 0.68 for ITGAL*02 (encoding HNA-5b). Interestingly, it was also found that rs2230433 variant deciding the HNA class 5 alleles, was highly prevalent (78.2%) in the Indian population compared with other global populations. This study presents the first comprehensive report of HNA allele and genotype frequencies in the Indian population using population genome datasets of 1029 individuals. Significant difference was observed in the prevalence of HNA5a and HNA5b in India in comparison to other global populations.
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Affiliation(s)
- Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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19
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Jiang X, Yuan X, Li Y, Zhang T, Chen L, Bao X, He J. Use of next-generation sequencing to detect polymorphism of 11 HLA allele loci in the Chinese Han population and variance from other common and well-documented lists. HLA 2023; 101:222-227. [PMID: 36480173 DOI: 10.1111/tan.14932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The focus of this study was to analyze polymorphisms in the HLA gene at 11 loci in 4845 Chinese Han populations using next-generation sequencing methods, and to compare common and well-documented (CWD) allelic differences between China and other CWD lists. A total of 44 DPB1 alleles, 13 DPA1 alleles, 20 DQA1 alleles and 19 DRB3/4/5 alleles were detected in this study. About 20%-50% of the CWD alleles in China differ from the American Society for Histocompatibility and Immunogenetics and European Federation for Immunogenetics (EFI) data. The revised list of HLA-CWD alleles in the Han population will provide additional data for the update of the IMGT/HLA database and contribute to a better understanding of hematopoietic stem cell transplantation and organ transplantation.
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Affiliation(s)
- Xue Jiang
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoni Yuan
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Li
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - TengTeng Zhang
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Luyao Chen
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaojing Bao
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun He
- Department of HLA Laboratory, Jiangsu Institute of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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20
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Manela C, Susanti R, Tjong DH, Yudianto A. DNA Polymorphism of 13 Autosomal Short Tandem Repeats (STR) Loci in Mentawai Populations. Pak J Biol Sci 2023; 26:101-107. [PMID: 37480266 DOI: 10.3923/pjbs.2023.101.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
<b>Background and Objective:</b> Indonesia consists of various ethnic groups with diverse cultures. However, research on allele frequencies and genetic variations of each ethnic group in Indonesia has not been well established. Therefore, a study was conducted on 13 STR loci panels to analyze the mentawai population as an enhancement of the Indonesian population's genetic data library and genetic variation. Mentawai is one of the Indonesian tribes who live on Mentawai Island, West Sumatera. <b>Materials and Methods:</b> The PrepFiler kit to extract DNA from blood and the GlobalFiler kit for amplifying the 13 loci were used. The genetic analyzer ABI PRISM 3500 was used to detect PCR products. Data were processed and analyzed by EasyDNA and FORSTAT software. <b>Results:</b> The allele frequency data for 13 autosomal loci in Mentawai populations were obtained. Expected heterozygosity was found with a minimum of 0.607 for TPOX and a maximum of 0.866 for FGA. Power of discrimination (PD) values ranges from TPOX (0.792) to FGA (0.968). Polymorphic information content (PIC) values for all loci were high, ranging from 0.642 for TPOX to 0.921 for vWA. Three off-ladder alleles in these findings were detected. Allele 6.3 at the TH01 loci and allele 14.2 at the D18S51 loci are exquisite. The mean expected heterozygosity and mean power of discrimination value across the 13 loci were 75.9 and 90.1%, indicating striking gene diversity. <b>Conclusion:</b> These 13 STR loci can be used for population genetic studies and forensic identification.
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21
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Eriksson S, Strandberg E, Johansson AM. Changes in genomic inbreeding and diversity over half a century in Swedish Red and Swedish Holstein dairy cattle. J Anim Breed Genet 2023; 140:295-303. [PMID: 36645266 DOI: 10.1111/jbg.12758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Swedish Red (SR) and Swedish Holstein (SH) are the dominating commercial dairy cattle breeds in Sweden. Both breeds have undergone substantial changes during the last half century due to intensive selection for breeding goal traits, but also resulting from increased international exchange of breeding animals and genetic drift. The aim of this study was to learn more about changes in genomic diversity and inbreeding in these two breeds over time. Therefore, semen samples from old bulls were genotyped using the 150K Genomic Profiler SNP array and combined with 50K SNP array genotype data, obtained for more recent bulls from the Nordic Cattle Genetic Evaluation. Different measures of level of homozygosity, genomic inbreeding, relatedness and changes in allele frequency were estimated for bulls born during different time periods from the 1950s until 2020. In total, more than 33,000 SNPs for 9737 SR and 5041 SH bulls were included in the analysis using PLINK v1.9. The results showed higher average homozygosity for SR than for SH bulls up to around 2000, but the difference was very small after that. The average inbreeding coefficients based on deviation from expected homozygosity as well as on runs of homozygosity decreased until the early 1980s in both breeds, whereafter they started to increase again for SH, but stayed more stable for SR. From the 1990s onwards, SH displayed higher average inbreeding coefficients than SR. In the last studied birth year group (2015-2020), the mean inbreeding coefficient based on runs of homozygosity was 5.9% for SH and 3.7% for SR. A principal component analysis showed a pattern of genetic relationships related to the birth year period of the bulls, illustrating the gradual change of the genetic material within each breed. The change in allele frequency over time was generally larger for SH than for SR. The results show that the inbreeding level was higher half a century ago than at present, and the inbreeding levels were lower than in some other studied populations. Still, the increase seen for inbreeding coefficients and homozygosity, especially in SH during recent years, should be considered in future breeding strategies.
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Affiliation(s)
- Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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22
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Hernández-Mejía DG, Páez-Gutiérrez IA, Dorsant Ardón V, Camacho Ramírez N, Mosquera M, Cendales PA, Camacho BA. Distributions of the HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 alleles and haplotype frequencies of 1763 stem cell donors in the Colombian Bone Marrow Registry typed by next-generation sequencing. Front Immunol 2023; 13:1057657. [PMID: 36700199 PMCID: PMC9869256 DOI: 10.3389/fimmu.2022.1057657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
The HLA compatibility continues to be the main limitation when finding compatible donors, especially if an identical match is not found within the patient's family group. The creation of bone marrow registries allowed a therapeutic option by identifying 10/10 compatible unrelated donors (URD). However, the availability and frequency of haplotypes and HLA alleles are different among ethnic groups and geographical areas, increasing the difficulty of finding identical matches in international registries. In this study, the HLA-A, -B, -C, -DRB1, and -DQB1 loci of 1763 donors registered in the Colombian Bone Marrow Registry were typed by next-generation sequencing. A total of 52 HLA-A, 111 HLA-B, 41 HLA-C, 47 HLA-DRB1, and 20 HLA-DQB1 alleles were identified. The 3 most frequent alleles for each loci were A*24:02g (20,8%), A*02:01g (16,1%), A*01:01g (7.06%); B*35:43g (7.69%), B*40:02g (7.18%), B*44:03g (6.07%); C*04:01g (15.40%), C*01:02g (10.49%), C*07:02g (10.44%); DRB1*04:07g (11.03%), DRB1*07:01g (9.78%), DRB1*08:02g (6.72%); DQB1*03:02g (20.96%), DQB1*03:01g (17.78%) and DQB1*02:01g (16.05%). A total of 497 HLA-A-C-B-DRB1-DQB1 haplotypes were observed with a frequency greater than or equal to 0.05% (> 0.05%); the haplotypes with the highest frequency were A*24:02g~B*35:43g~C*01:02g~DQB1*03:02g~DRB1*04:07g (3.34%), A*29:02g~B*44:03g~C*16:01g~DQB1*02:01g~DRB1*07:01g (2.04%), and A*01:01g~B*08:01g~C*07:01g~DQB1*02:01g~DRB1*03:01g (1.83%). This data will allow the new Colombian Bone Marrow Donor Registry to assess the genetic heterogeneity of the Colombian population and serve as a tool of interest for future searches of unrelated donors in the country.
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23
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
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24
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Xi P, Wang H, Zhong Z, Liu S, Tang J, Guo C, Dai P. rs144012689 is a highly specific representative marker of HLA-B*15:02 in the Chinese population. Pharmacogenomics 2022; 23:835-845. [PMID: 36169168 DOI: 10.2217/pgs-2022-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Objective: To develop an accurate and rapid real-time PCR technique for HLA-B*15:02 genotyping and investigate HLA-B*15:02 allele frequency in four ethnic populations in China. Materials & methods: Based on the highly specific representative markers, a real-time PCR assay was developed for HLA-B*15:02 genotyping, and HLA-B*15:02 allele frequencies were screened in four ethnic populations of China. Sequence-based typing was used to validate the accuracy of the assay. Results: The sensitivity and specificity of the assay were 100%, and the detection limit was 0.2 ng. The frequency of HLA-B*15:02 alleles distributed in the Bouyei population was significantly higher than in the Han group (p < 0.01). Neither the Tibetan nor the Uyghur population carried the HLA-B*15:02 haplotype. Conclusion: The authors developed an accurate HLA-B*15:02 genotyping method for evaluating the risk of adverse drug reactions induced by carbamazepine in various ethnic populations in China.
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Affiliation(s)
- Pei Xi
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
| | - Hao Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Zihua Zhong
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Shihui Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Jiaxuan Tang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Chunli Guo
- Pulmonary and Critical Care Medicine, Tongchuan People's Hospital, Tongchuan, Shaanxi Province, People's Republic of China
| | - Penggai Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
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25
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Németh S, Kriegshäuser G, Hovhannesyan K, Hayrapetyan H, Oberkanins C, Sarkisian T. Very low frequency of the lactase persistence allele LCT-13910T in the Armenian population. Ann Hum Biol 2022; 49:260-262. [PMID: 36129808 DOI: 10.1080/03014460.2022.2126887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Primary lactose malabsorption is characterised by a down-regulation of lactase activity after weaning and inability to digest lactose in adulthood. It has been suggested that the historical introduction of dairying led to a positive selection for lactase persistence variants in a regulatory region upstream of the LCT gene. Here, we genotyped 202 Armenian subjects for LCT-13910T, a lactase persistence variant which is widespread in Europeans. The homozygous C/C genotype associated with primary hypolactasia, the heterozygous C/T and the homozygous T/T lactase persistence genotypes were found in 191 (94.6%), 11 (5.4%), and 0 (0.0%) samples, respectively. The frequency for the LCT-13910*T allele was 2.7%. The observed allele frequency of 2.7% for LCT-13910T is even lower than previously reported and supports current phenotypic data about lactose malabsorption in Armenia.
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Affiliation(s)
| | | | | | - Hasmik Hayrapetyan
- Center of Medical Genetics and Primary Health Care, Yerevan, Armenia.,Department of Medical Genetics, Yerevan State Medical University, Yerevan, Armenia
| | | | - Tamara Sarkisian
- Center of Medical Genetics and Primary Health Care, Yerevan, Armenia.,Department of Medical Genetics, Yerevan State Medical University, Yerevan, Armenia
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26
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Wang J. MLNe: Simulating and Estimating Effective Size and Migration Rate from Temporal Changes in Allele Frequencies. J Hered 2022; 113:563-567. [PMID: 35932284 DOI: 10.1093/jhered/esac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022] Open
Abstract
In studies of molecular ecology, conservation biology and evolutionary biology, the current or recent effective size (Ne) of a population is frequently estimated from the marker genotype data of two or more temporally spaced samples of individuals taken from the population. Despite the developments of numerous Bayesian, likelihood and moment estimators, only a couple of them can use both temporally and spatially spaced samples of individuals to estimate jointly the effective size (Ne) of and the migration rate (m) into a population. In this note I describe new implementations of these joint estimators of Ne and m in software MLNe which runs on multiple platforms (Windows, Mac, Linux) with or without a graphical user interface (GUI), has an integrated simulation module to simulate genotype data for investigating the impacts of various factors (such as sample size and sampling interval) on estimation precision and accuracy, exploits both Message Passing Interface (MPI) and openMP for parallel computations using multiple cores and nodes to speed up analysis. The program does not require data pre-processing and accepts multiple formats of a file of original genotype data and a file of parameters as input. The GUI facilitates data and parameter inputs and produces publication-quality output graphs, while the non-GUI version of software is convenient for batch analysis of multiple datasets as in simulations. MLNe will help advance the analysis of temporal genetic marker data for estimating Ne of and m between populations, which are important parameters that will help biologists for the conservation management of natural and managed populations. MLNe can be downloaded free from the website http://www.zsl.org/science/research/software/.
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Affiliation(s)
- Jinliang Wang
- Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom
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Que TN, Khanh NB, Tung PD, Hang PTL, Van Anh NT, Thang ND. Frequency and distribution of HLA-DQB1 alleles from 2076 cord blood samples of the Vietnamese cohort. Int J Immunogenet 2022; 49:340-344. [PMID: 35916345 DOI: 10.1111/iji.12592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Human leucocyte antigen (HLA) alleles are very diverse and characterized by ethnicity. To date, information about the frequencies and distributions of HLA alleles among the Vietnamese population is still limited. In this study, HLA-DQB1 alleles of 2076 cord blood units from individuals belonging to Vietnam's Kinh ethnic people were genotyped using Luminex-based polymerase chain reaction sequence-specific oligonucleotide. The results of the study demonstrated that there were 23 alleles on the locus HLA-DQB1. Among those, there were six alleles with high frequencies of over 5%, including DQB1* 03:01 (35.9%), DQB1* 05:01 (12.8%), DQB1* 03:03 (12.2%); DQB1* 06:01 (7.20%), DQB1* 05:02 (6.62%) and DQB1* 02:01 (5.30%) and five rare alleles with low frequencies of below 0.1%. More importantly, this study for the first time reported the presence of two new rare alleles including DQB1* 01:01 and DQB1* 01:02. Conclusively, this study provided significant information about HLA-DQB1 alleles for further investigations and clinical applications.
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Affiliation(s)
- Tran Ngoc Que
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam.,Department of Hematology, Hanoi Medical University, Hanoi, Vietnam
| | - Nguyen Ba Khanh
- Stem Cell Bank, National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam.,Department of Hematology, Hanoi Medical University, Hanoi, Vietnam
| | - Pham Dinh Tung
- Department of Probability and Statistics, Faculty of Mathematics-Mechanics-Informatics, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Pham Thi Luong Hang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
| | - Nguyen Thi Van Anh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
| | - Nguyen Dinh Thang
- Faculty of Biology, VNU University of Science, Vietnam National University-Hanoi, Hanoi, Vietnam
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28
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Nauheim D, Moskal D, Renslo B, Chadwick M, Jiang W, Yeo CJ, Nevler A, Bowne W, Lavu H. KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer. J Surg Oncol 2022; 126:314-321. [PMID: 35333412 DOI: 10.1002/jso.26860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/05/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) provides information on genetic mutations and mutant allele frequency in tumor specimens. We investigated the prognostic significance of KRAS mutant allele frequency in patients with right-sided pancreatic ductal adenocarcinoma (PDAC) treated with surgical resection. METHODS A retrospective study reviewed patients who underwent surgical resection for PDAC and analyzed tumors with an in-house mutational panel. Microdissected samples were studied using an NGS-based assay to detect over 200 hotspot mutations in 42 genes (Pan42) commonly involved in PDAC. RESULTS A total of 144 PDAC right-sided surgical patients with a Pan42 panel were evaluated between 2015 and 2020; 121 patients (84%) harbored a KRAS mutation. Detected mutant allele frequencies were categorized as less than 20% (low mKRAS, n = 92) or greater than or equal to 20% (high mKRAS, n = 29). High mKRAS (KRAS ≥ 20%) patients were noted to have shorter disease-free survival after surgery (11.5 ± 2.1 vs. 19.5 ± 3.5 months, p = 0.03), more advanced tumor stage (p = 0.02), larger tumors (3.6 vs. 2.7 cm, p = 0.001), greater tumor cellularity (26% vs. 18%, p = 0.001), and higher rate of distant recurrence (p = 0.03) than low mKRAS patients. CONCLUSION This study demonstrates the importance of KRAS mutant allele frequency on pathological characteristics and prognosis in right-sided PDAC treated with surgery.
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Affiliation(s)
- David Nauheim
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Moskal
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Bryan Renslo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matthew Chadwick
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wei Jiang
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles J Yeo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Avinoam Nevler
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wilbur Bowne
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Harish Lavu
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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29
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Anderson RE, Graham ED, Huber JA, Tully BJ. Microbial Populations Are Shaped by Dispersal and Recombination in a Low Biomass Subseafloor Habitat. mBio 2022;:e0035422. [PMID: 35913164 DOI: 10.1128/mbio.00354-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.
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30
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Chentoufi AA, Uyar FA, Chentoufi HA, Alzahrani K, Paz M, Bahnassy A, Elyamany G, Elghazaly A. HLA Diversity in Saudi Population: High Frequency of Homozygous HLA Alleles and Haplotypes. Front Genet 2022; 13:898235. [PMID: 35754807 PMCID: PMC9218871 DOI: 10.3389/fgene.2022.898235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Human leukocyte antigens (HLA) diversity has a tremendous impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions. Here, we conducted a retrospective study of HLA class I and class II homozygosity at allelic and haplotype levels in unrelated individuals genotyped from 2012 to 2016 in a tertiary hospital in the capital of Saudi Arabia. Among 5,000 individuals, 2,773 individuals meet inclusion criteria and were retrospectively analyzed for HLA-A, -B, -C-DRB1, and -DQB1 homozygosity at allelic and haplotype levels. HLA molecular typing was performed using a commercial reverse sequence-specific oligonucleotide (rSSO) kit. We were able to identify 15 HLA-A, 20 HLA-B, 11 HLA-C, 13 HLA-DRB1, and five HLA-DQB1 homozygous alleles demonstrating a very low genetic diversity in the Saudi population. The highest homozygosity in HLA class I was found in locus C followed by A and B (20.3% > 16.1% > 15.5%; p < 0.001) where the most homozygote alleles were A*02 (9.2%), B*51 and B*50 (5.7% and 3.7%), and C*07, C*06, and C*15 (7.2%, 5.48%, and 3.3%) and in HLA class II, the highest homozygosity was found in locus DQB1 compared to DRB1 (31.71% > 19.2%; p < 0.001), with the most common homozygote alleles being DRB1*07 and DRB1*04 (5.33% and 4.2%) and DQB1*02, DQB1*06, and DQB1*03 (13.55%, 7.92%, and 7.64%). The frequency of finding an individual with one homozygote allele was (24.6%), two homozygote alleles (13.5%), three homozygote alleles (4.7%), four homozygote alleles (3.4%), and five alleles were (4.8%). The most frequent homozygote haplotypes are A*23∼C*06∼B*50∼DRB1*07∼DQB1*02 and A*02∼C*06∼B*50∼DRB1*07∼DQB1*02. This study shows low diversity of both class I and II alleles and haplotypes in the Saudi population, which would have a significant impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host-pathogen interactions.
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Affiliation(s)
- Aziz Alami Chentoufi
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - F Aytül Uyar
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | | | - Maria Paz
- King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ghaleb Elyamany
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Assem Elghazaly
- King Fahad Medical City, Riyadh, Saudi Arabia.,Department of Hematology/Oncology, King Saud Medical City, Riyadh, Saudi Arabia
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31
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Alcala N, Rosenberg NA. Mathematical constraints on FST: multiallelic markers in arbitrarily many populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200414. [PMID: 35430885 PMCID: PMC9014193 DOI: 10.1098/rstb.2020.0414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/23/2021] [Indexed: 11/12/2022] Open
Abstract
Interpretations of values of the FST measure of genetic differentiation rely on an understanding of its mathematical constraints. Previously, it has been shown that FST values computed from a biallelic locus in a set of multiple populations and FST values computed from a multiallelic locus in a pair of populations are mathematically constrained as a function of the frequency of the allele that is most frequent across populations. We generalize from these cases to report here the mathematical constraint on FST given the frequency M of the most frequent allele at a multiallelic locus in a set of multiple populations. Using coalescent simulations of an island model of migration with an infinitely-many-alleles mutation model, we argue that the joint distribution of FST and M helps in disentangling the separate influences of mutation and migration on FST. Finally, we show that our results explain a puzzling pattern of microsatellite differentiation: the lower FST in an interspecific comparison between humans and chimpanzees than in the comparison of chimpanzee populations. We discuss the implications of our results for the use of FST. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.
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Affiliation(s)
- Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genetic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization, Lyon 69008, France
| | - Noah A. Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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32
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Schipper T, Ohlsson Å, Longeri M, Hayward JJ, Mouttham L, Ferrari P, Smets P, Ljungvall I, Häggström J, Stern JA, Lyons LA, Peelman LJ, Broeckx BJG. The TNNT2:c.95-108G>A variant is common in Maine Coons and shows no association with hypertrophic cardiomyopathy. Anim Genet 2022; 53:526-529. [PMID: 35634705 DOI: 10.1111/age.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) is a common and potentially fatal heart disease in many cat breeds. An intronic variant in TNNT2, c.95-108G>A, was recently reported as the cause of HCM in the Maine Coon. The aim of this study was to determine this variant's allele frequency in different populations and its possible association with HCM. Based on 160 Maine Coon samples collected in Belgium, Italy, Sweden and the USA, the variant's allele frequency was estimated to be 0.32. Analysis of the 99 Lives feline whole genome sequencing database showed that the TNNT2 variant also occurs in other breeds, as well as mixed-breed cats. Comparison of 31 affected and 58 healthy cats did not reveal significantly increased odds for HCM in homozygotes. Based on the combined evidence and in agreement with the standards and guidelines for the interpretation of sequence variants, this variant is currently classified as a variant of unknown significance and should not be used for breeding decisions regarding HCM.
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Affiliation(s)
- Tom Schipper
- Department of Veterinary and Biosciences, Ghent University, Merelbeke, Belgium
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Longeri
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | - Jessica J Hayward
- Department of Biomedical Sciences and Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Lara Mouttham
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Paolo Ferrari
- Osservatorio Veterinario Italiano Cardiopatie, Azzano S. Paolo, Italy
| | - Pascale Smets
- Small Animal Department, Ghent University, Merelbeke, Belgium
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Joshua A Stern
- Department of Medicine and Epidemiology, University of California - Davis, Davis, California, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri, USA
| | - Luc J Peelman
- Department of Veterinary and Biosciences, Ghent University, Merelbeke, Belgium
| | - Bart J G Broeckx
- Department of Veterinary and Biosciences, Ghent University, Merelbeke, Belgium
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33
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Kaja E, Lejman A, Sielski D, Sypniewski M, Gambin T, Dawidziuk M, Suchocki T, Golik P, Wojtaszewska M, Mroczek M, Stępień M, Szyda J, Lisiak-Teodorczyk K, Wolbach F, Kołodziejska D, Ferdyn K, Dąbrowski M, Woźna A, Żytkiewicz M, Bodora-Troińska A, Elikowski W, Król ZJ, Zaczyński A, Pawlak A, Gil R, Wierzba W, Dobosz P, Zawadzka K, Zawadzki P, Sztromwasser P. The Thousand Polish Genomes-A Database of Polish Variant Allele Frequencies. Int J Mol Sci 2022; 23:4532. [PMID: 35562925 DOI: 10.3390/ijms23094532] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Although Slavic populations account for over 4.5% of world inhabitants, no centralised, open-source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for clinical genetics, biomedical research, as well as archeological and historical studies. The Polish population, which is homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a genetic reference for the Slavic nations. In this study, we analysed whole genomes of 1222 Poles to identify and genotype a wide spectrum of genomic variation, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups, and de novo variants. Common variant analyses showed that the Polish cohort is highly homogenous and shares ancestry with other European populations. In rare variant analyses, we identified 32 autosomal-recessive genes with significantly different frequencies of pathogenic alleles in the Polish population as compared to the non-Finish Europeans, including C2, TGM5, NUP93, C19orf12, and PROP1. The allele frequencies for small and structural variants, calculated for 1076 unrelated individuals, are released publicly as The Thousand Polish Genomes database, and will contribute to the worldwide genomic resources available to researchers and clinicians.
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34
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Islam MS, Takagi M, Lee KW, Chang HS, Okawa H, Yunus M, Lestari TD, Tacharina MR, Pervin S, Rakib TM, Yabuki A, Yamato O. Frequency of an X-Linked Maternal Variant of the Bovine FOXP3 Gene Associated with Infertility in Different Cattle Breeds: A Pilot Study. Animals (Basel) 2022; 12. [PMID: 35454290 DOI: 10.3390/ani12081044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Immune adaptation plays an essential role in determining pregnancy, which has been shown to be dependent on sufficient immunological tolerance mediated by FOXP3+ regulatory T cells. Recently, an X-linked maternal single-nucleotide polymorphism (SNP), located 2175 base pairs upstream of the start codon in the bovine FOXP3 gene (NC_037357.1: g.87298881A>G, rs135720414), was identified in Japanese Black (JB: Bos taurus) cows in association with recurrent infertility. However, with the exception of JB cows, the frequency of this SNP has yet to be studied in other cow populations. In this study, we thus aimed to evaluate the frequency of this SNP in different cow breeds. Between 2018 and 2021, a total of 809 DNA samples were obtained from 581 JB, 73 Holstein Friesian (HF: B. taurus), 125 Korean Hanwoo (KH: B. taurus coreanae), and 30 Indonesian Madura (IM: a crossbreed between B. indicus and B. javanicus) cows, which were genotyped using a TaqMan probe-based real-time polymerase chain reaction assay designed in this study. The frequency of the G allele was found to be relatively high in local IM (0.700), moderate in dairy HF (0.466), and low in beef JB (0.250) and KH (0.112) cows, with differences in the frequencies between each group being shown to be statistically significant (p < 0.005) using Fisher’s exact test. The results obtained in this study indicate that the G allele frequencies of the identified the SNP differ markedly in different breeds of taurine and indicine cattle. Given these findings, it would thus be important to evaluate the relationships between high frequencies of the G allele and infertility in different breeds.
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35
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Santiago González JC, Kerns DL, Head GP, Yang F. Status of Cry1Ac and Cry2Ab2 resistance in field populations of Helicoverpa zea in Texas, USA. Insect Sci 2022; 29:487-495. [PMID: 34258865 DOI: 10.1111/1744-7917.12947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Helicoverpa zea is a major target pest of Bt corn and Bt cotton. Field-evolved resistance of H. zea to Cry1 and Cry2 proteins has been widely reported in the United States. Understanding the frequency of resistance alleles in a target insect is critical for Bt resistance management. Despite multiple cases of practical resistance to Cry proteins having been documented in H. zea, there are no data on the current status of alleles conferring resistance to Cry1Ac and Cry2Ab2 in field populations of this pest. During 2018-2019, a total of 106 F2 families for Cry1Ac and 120 F2 families for Cry2Ab2 were established using mass mating and light trap strategy. We screened 13,568 and 15,360 neonates using a discriminatory dose of Cry1Ac and Cry2Ab2, respectively. The results showed that 93.4% and 35.0% of the F2 families could survive on the discriminatory dose of Cry1Ac and Cry2Ab2, respectively. The estimated resistance allele frequency for Cry1Ac in H. zea ranged from 0.4150 to 0.4975 and for Cry2Ab2 ranged from 0.1097 and 0.1228. These data indicate that the frequency of alleles conferring resistance to Cry1 and Cry2 proteins in H. zea in Texas are high. In addition, our data suggest the resistance to Cry1Ac and Cry2Ab2 in the screened families of H. zea varies from recessive to dominant. The information in this study provides precise estimates of Cry resistance allele frequencies in H. zea and increases our understanding of the risks to the sustainability of Bt crops.
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Affiliation(s)
| | - David L Kerns
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | | | - Fei Yang
- Department of Entomology, Texas A&M University, College Station, Texas, USA
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36
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Zhang C, Wang J, Xiao X, Wang D, Yuan Z, Zhang X, Sun W, Yu S. Fine Mapping of Two Interacting Loci for Transmission Ratio Distortion in Rice ( Oryza sativa L.). Front Plant Sci 2022; 13:866276. [PMID: 35422832 PMCID: PMC9002327 DOI: 10.3389/fpls.2022.866276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Transmission ratio distortion (TRD) denotes the observed allelic or genotypic frequency deviation from the expected Mendelian segregation ratios in the offspring of a heterozygote. TRD can severely hamper gene flow between and within rice species. Here, we report the fine mapping and characterization of two loci (TRD4.1 and TRD4.2) for TRD using large F2 segregating populations, which are derived from rice chromosome segment substitution lines, each containing a particular genomic segment introduced from the japonica cultivar Nipponbare (NIP) into the indica cultivar Zhenshan (ZS97). The two loci exhibited a preferential transmission of ZS97 alleles in the derived progeny. Reciprocal crossing experiments using near-isogenic lines harboring three different alleles at TRD4.1 suggest that the gene causes male gametic selection. Moreover, the transmission bias of TRD4.2 was diminished in heterozygotes when they carried homozygous TRD4.1 ZS97. This indicates an epistatic interaction between these two loci. TRD4.2 was mapped into a 35-kb region encompassing one candidate gene that is specifically expressed in the reproductive organs in rice. These findings broaden the understanding of the genetic mechanisms of TRD and offer an approach to overcome the barrier of gene flow between the subspecies in rice, thus facilitating rice improvement by introgression breeding.
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Affiliation(s)
- Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jilin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiongfeng Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaodan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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37
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Tian J, Zhang J, Yang Z, Feng S, Li S, Ren S, Shi J, Hou X, Xue X, Yang B, Xu H, Guo J. Genetic Epidemiology of Medication Safety and Efficacy Related Variants in the Central Han Chinese Population With Whole Genome Sequencing. Front Pharmacol 2022; 12:790832. [PMID: 35280256 PMCID: PMC8906509 DOI: 10.3389/fphar.2021.790832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/14/2021] [Indexed: 12/22/2022] Open
Abstract
Medication safety and efficacy-related pharmacogenomic research play a critical role in precision medicine. This study comprehensively analyzed the pharmacogenomic profiles of the central Han Chinese population in the context of medication safety and efficacy and compared them with other global populations. The ultimate goal is to improve medical treatment guidelines. We performed whole-genome sequencing in 487 Han Chinese individuals and investigated the allele frequencies of pharmacogenetic variants in 1,731 drug response-related genes. We identified 2,139 (81.18%) previously reported variants in our population with annotations in the PharmGKB database. The allele frequencies of these 2,139 clinical-related variants were similar to those in other East Asian populations but different from those in other global populations. We predicted the functional effects of nonsynonymous variants in the 1,731 pharmacogenes and identified 1,281 novel and 4,442 previously reported deleterious variants. Of the 1,281 novel deleterious variants, five are common variants with an allele frequency >5%, and the rest are rare variants with an allele frequency <5%. Of the 4,442 known deleterious variants, the allele frequencies were found to differ from those in other populations, of which 146 are common variants. In addition, we found many variants in non-coding regions, the functions of which require further investigation. This study compiled a large amount of data on pharmacogenomic variants in the central Han Chinese population. At the same time, it provides insight into the role of pharmacogenomic variants in clinical medication safety and efficacy.
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Affiliation(s)
- Junbo Tian
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jing Zhang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zengguang Yang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Shuaisheng Feng
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Shujuan Li
- Department of Pharmacy, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shiqi Ren
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianxiang Shi
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinyue Hou
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xia Xue
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Bei Yang
- School of Information Engineering, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Jiancheng Guo
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Yousuf AM, Kannu FA, Youssouf TM, Alsuhaimi FN, Aljohani AM, Alsehli FH, Khabour OF, Almutawif YA, Najim MA, Mahmood HA. Lack of association between fat mass and obesity-associated genetic variant (rs8050136) and type 2 diabetes mellitus. Saudi Med J 2022; 43:132-138. [PMID: 35110337 PMCID: PMC9127913 DOI: 10.15537/smj.2022.43.2.20210822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives: To study the genotype and allele frequency of the fat mass and obesity-associated (FTO) rs8050136 A>C genetic variant and investigate its association with type 2 diabetes mekkitus (T2DM) parameters. Methods: This study was carried out on 118 diabetic patients and 106 healthy individuals (control) from Prince Mohammed bin Abdulaziz Hospital, Al Madinah Al Munawarah, Saudi Arabia. The TaqMan single-nucleotide polymorphism (SNP)genotyping assay was used for rs8050136 genotyping. Results: The frequency of the genotype AA was the same among T2DM and healthy control groups (21%). However, the frequency of genotype CC was 19.5% in T2DM patients and 24.5% in control individuals. There was no significant association between FTO SNP rs8050136 and an increased risk of T2DM. Furthermore, there was no association between the risk AA genotype and fasting blood glucose (p=0.092), glycated hemoglobin (p=0.177), or body mass index (p=0.561). Conclusion: Our findings show that the FTO rs8050136 A>C variant is not associated with T2DM in the Saudi population.
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Affiliation(s)
- Amjad M. Yousuf
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
- Address correspondence and reprint request to: Dr. Amjad M. Yousuf, Assistant Professor, Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Al Madinah Al Munawarah, Kingdom of Saudi Arabia. E-mail: ORCID: https://orcid.org/0000-0003-2573-8645
| | - Firoz A. Kannu
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Talha M. Youssouf
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Fatimah N. Alsuhaimi
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Abdulaziz M. Aljohani
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Fayez H. Alsehli
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Omar F. Khabour
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Yahya A. Almutawif
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Mustafa A. Najim
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Hatem A. Mahmood
- From the Department of Medical Laboratories Technology (Yousuf, Kannu, Almutawif, Najim), College of Applied Medical Sciences, Taibah University; from the General Directorate of Laboratories and Blood Banks (Alsehli), Ministry of Health; from the Department of Medicine (Youssouf, Alsuhaimi, Mahmood), from Pathology and Laboratory Medicine Department (Aljohani), Prince Mohammed Bin Abdulaziz Hospital, Al Madinah Al Munawarah, Kingdom of Saudi Arabia; and from the Department of Medical Laboratory Sciences (Khabour), Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan.
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Abstract
RNA translation is the rate-limiting step when cells synthesize proteins. Elevating translation efficiency (TE) is intuitively beneficial. Particularly, when viruses invade host cells, how to compete with endogenous RNAs for efficient translation is a major issue to be resolved. We collected millions of worldwide SARS-CoV-2 sequences during the past year and traced the dynamics of allele frequency of every mutation. We defined adaptive and deleterious mutations according to the rise and fall of their frequencies along time. For 5ʹUTR and synonymous mutations in SARS-CoV-2, the selection on TE is evident near start codons. Adaptive mutations generally decrease GC content while deleterious mutations increase GC content. This trend fades away with increasing distance to start codons. Mutations decreasing GC content near start codons would unravel the complex RNA structure and facilitate translation initiation, which are beneficial to SARS-CoV-2, and vice versa. During this evolutionary arms race between human and virus, SARS-CoV-2 tries to improve its cis elements to compete with host RNAs for rapid translation.
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Affiliation(s)
- Lin Zhu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Qi Wang
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Weiyu Zhang
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China.,Peking University Applied Lithotripsy Institute, Peking University People's Hospital, Xicheng, Beijing, China
| | - Hao Hu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Kexin Xu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
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40
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Dash HR, Vajpayee K, Agarwal R, Gang A, Shukla R, Srivastava A. Evaluation of diallelic STR markers with inter-population allelic database for their usefulness in paternity trios in the Central Indian population. Ann Hum Biol 2021; 48:605-613. [PMID: 34866517 DOI: 10.1080/03014460.2021.2014567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most of the forensic DNA laboratories have migrated to new generation STR kits of 6 dye chemistry with more than 20 autosomal STRs. The population-specific databases of such STR markers are lacking in many regions. AIM To evaluate the effect of the inter-population database in 100 paternity trios with no inconsistencies at 23 STRs. SUBJECTS AND METHODS 100 paternity trios were evaluated considering inter-population allelic frequency values for calculation of Combined Paternity Index (CPI) and Probability of Paternity (POP). RESULTS No significant variation (p < 0.05) among the allele frequencies at the interpopulation level was observed. The number of obligate alleles and the likelihood of transferring obligate alleles from the putative father showed a positive correlation (p < 0.005) with Power of Discrimination (PD), Polymorphic Information Content (PIC), Power of Exclusion (PE), Paternity Index (PI), Observed and Expected Heterozygosity (Ho and He), and a statistically significant negative correlation (p < 0.005) with Matching Probability (Pm). The average Combined Paternity Index (CPI) and Probability of Paternity (POP) did not show any statistically significant difference (p < 0.05) at the interpopulation level. CONCLUSION The allelic database showed no effect on the CPI and POP in 100 paternity trios. This suggests no urgent need for using population-specific databases for statistical evaluation of paternity trios without inconsistencies.
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Affiliation(s)
| | - Kamayani Vajpayee
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India.,Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India
| | - Anubha Gang
- Regional Forensic Science Laboratory, Indore, India
| | - Ritesh Shukla
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, India
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41
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Gudmundsson S, Singer-Berk M, Watts NA, Phu W, Goodrich JK, Solomonson M, Rehm HL, MacArthur DG, O'Donnell-Luria A. Variant interpretation using population databases: Lessons from gnomAD. Hum Mutat 2021; 43:1012-1030. [PMID: 34859531 PMCID: PMC9160216 DOI: 10.1002/humu.24309] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/02/2021] [Accepted: 11/28/2021] [Indexed: 01/22/2023]
Abstract
Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery of new disease-gene relationships. The Genome Aggregation Database (gnomAD) is currently the largest and most widely used publicly available collection of population variation from harmonized sequencing data. The data is available through the online gnomAD browser (https://gnomad.broadinstitute.org/) that enables rapid and intuitive variant analysis. This review provides guidance on the content of the gnomAD browser, and its usage for variant and gene interpretation. We introduce key features including allele frequency, per-base expression levels, constraint scores, and variant co-occurrence, alongside guidance on how to use these in analysis, with a focus on the interpretation of candidate variants and novel genes in rare disease.
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Affiliation(s)
- Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julia K Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, New South Wales, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
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42
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Haenel Q, Guerard L, MacColl ADC, Berner D. The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish. Mol Ecol 2021; 31:811-821. [PMID: 34753205 PMCID: PMC9299253 DOI: 10.1111/mec.16269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long‐term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat—nutrient‐depleted acidic lakes—based on whole‐genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic‐adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds.
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Affiliation(s)
- Quiterie Haenel
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Guerard
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Daniel Berner
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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43
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Yamada A, Sugimura M, Kuramoto T. Genetic polymorphism of bovine beta-casein gene in Japanese dairy farm herds. Anim Sci J 2021; 92:e13644. [PMID: 34626147 PMCID: PMC9286554 DOI: 10.1111/asj.13644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/04/2021] [Accepted: 09/17/2021] [Indexed: 12/28/2022]
Abstract
The aim of this study was to investigate beta‐casein polymorphism among 320 Japanese cows sampled from eight dairy farms. We used a newly‐developed genotyping method that involved collecting DNA from hairs and a Cycleave polymerase chain reaction (PCR) assay to detect the A1, A2, and B variants. Results revealed the presence of five genotypes (A1A1, A2A2, A1A2, A1B, and A2B). We found that the most common genotype was A2A2 (0.42), followed by A1A2 (0.39) and A1A1 (0.11). The A1B and A2B genotypes were less frequent (<0.05). The frequencies of alleles A1, A2, and B were calculated to be 0.32, 0.64, and 0.04, respectively. Our study is the first to show the current status of beta‐casein polymorphisms in Japanese dairy farms. Given the adverse effects of A1 beta‐casein on human health, attempts have been made to develop herds consisting solely of A2A2 cows. Our study provides a reference for improving cow populations in Japanese dairy farms. The Cycleave PCR‐based assay we developed here can be used for rapid and reliable genotyping of bovine beta‐casein.
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Affiliation(s)
- Asaha Yamada
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Miyu Sugimura
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Takashi Kuramoto
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
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44
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Jeon S, Blazyte A, Yoon C, Ryu H, Jeon Y, Bhak Y, Bolser D, Manica A, Shin ES, Cho YS, Kim BC, Ryoo N, Choi H, Bhak J. Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates. Mol Cells 2021; 44:680-687. [PMID: 34588322 PMCID: PMC8490206 DOI: 10.14348/molcells.2021.2249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/14/2021] [Accepted: 07/10/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Hyojung Ryu
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | | | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Korea
| | | | | | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu 42601, Korea
| | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
- Geromics, Ltd., Cambridge CB1 3NF, UK
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Korea
- Clinomics, Inc., Ulsan 44919, Korea
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45
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Seitz S, Lange V, Norman PJ, Sauter J, Schmidt AH. Estimating HLA haplotype frequencies from homozygous individuals - A Technical Report. Int J Immunogenet 2021; 48:490-495. [PMID: 34570965 PMCID: PMC9131737 DOI: 10.1111/iji.12553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/31/2023]
Abstract
We estimated HLA haplotype frequencies based on individuals homozygous for 4, 5 or 6 loci. Validation of our approach using a sample of over 3.4 million German individuals was successful. Compared to an expectation‐maximization algorithm, the errors were larger. However, our approach allows the unequivocal detection of rare haplotypes.
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Affiliation(s)
| | | | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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46
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Yoon BW, Shin HT, Seo J. Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group. Genes (Basel) 2021; 12:genes12101530. [PMID: 34680925 PMCID: PMC8536051 DOI: 10.3390/genes12101530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 01/08/2023] Open
Abstract
The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse ancestry. We collected 320 single-nucleotide polymorphisms (SNPs) associated with vitamin D concentrations from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact tests to assess the significance of the enrichment or depletion of the effect allele at a given SNP in the database. In addition, we calculated the SNP-based genetic risk score (GRS) and performed correlation analysis with vitamin D concentration that included latitude. European, American, and South Asian populations showed similar heatmap patterns, whereas African, East Asian, and Korean populations had distinct ones. The GRS calculated from allele frequencies of vitamin D concentration was highest among Europeans, followed by East Asians and Africans. In addition, the difference in vitamin D concentration was highly correlated with genetic factors rather than latitude effects.
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Affiliation(s)
- Byung-Woo Yoon
- Division of Oncology, Department of Internal Medicine, Inje University Seoul Paik Hospital, Seoul 04551, Korea;
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University School of Medicine, Incheon 22212, Korea;
| | - Jehyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 05368, Korea
- Correspondence: ; Tel.: +82-2-2225-1445; Fax: +82-2-2225-3950
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47
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Abstract
The prevalence of myopia, or nearsightedness, has skyrocketed in the past few decades, creating a public health crisis that is commonly attributed to lifestyle changes. Here we report an overall increase in the frequencies of myopia-associated mutant alleles over 25 years among participants of the UK Biobank. Although myopia itself appears to be selected against, many of the mutant alleles are associated with reproductive benefits, suggesting that reproduction-related selection inadvertently contributes to the myopia epidemic. We estimate that, in the UK alone, natural selection adds more than 100 000 myopia cases per generation, and argue that antagonistic pleiotropy be broadly considered in explaining the spreads of apparently disadvantageous phenotypes in humans and beyond.
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Affiliation(s)
- Erping Long
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Choe W, Chae JD, Yang JJ, Hwang SH, Choi SE, Oh HB. Identification of 8-Digit HLA-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in Koreans Using the One Lambda AllType Next-Generation Sequencing Kit. Ann Lab Med 2021; 41:310-317. [PMID: 33303716 PMCID: PMC7748103 DOI: 10.3343/alm.2021.41.3.310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/13/2020] [Accepted: 11/26/2020] [Indexed: 12/02/2022] Open
Abstract
Background Recent studies have successfully implemented next-generation sequencing (NGS) in HLA typing. We performed HLA NGS in a Korean population to estimate HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies up to an 8-digit resolution, which might be useful for an extended application of HLA results. Methods A total of 128 samples collected from healthy unrelated Korean adults, previously subjected to Sanger sequencing for 6-digit HLA analysis, were used. NGS was performed for HLA-A, -B, -C, and -DRB1 using the AllType NGS kit (One Lambda, West Hills, CA, USA), Ion Torrent S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), and Type Steam Visual NGS analysis software (One Lambda). Results Eight HLA alleles showed frequencies of ≥10% in the Korean population, namely, A*24:02:01:01 (19.5%), A*33:03:01 (15.6%), A*02:01:01:01 (14.5%), A*11:01:01:01 (13.3%), B*15:01:01:01 (10.2%), C*01:02:01 (19.9%), C*03:04:01:02 (11.3%), and DRB1*09:01:02 (10.2%). Nine previous 6-digit HLA alleles were further identified as two or more 8-digit HLA alleles. Of these, eight alleles (A*24:02:01, B*35:01:01, B*40:01:02, B*55:02:01, B*58:01:01, C*03:02:02, C*07:02:01, and DRB1*07:01:01) were identified as two 8-digit HLA alleles, and one allele (B*51:01:01) was identified as three 8-digit HLA alleles. The most frequent four-loci haplotype was HLA-A*33:03:01-B*44:03:01:01-C*14:03-DRB1*13:02:01. Conclusions We identified 8-digit HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a healthy Korean population using NGS. These new data can be used as a representative Korean data for further disease-related HLA type analysis.
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Affiliation(s)
- Wonho Choe
- Department of Laboratory Medicine, Eulji University School of Medicine, Seoul, Korea
| | - Jeong-Don Chae
- Department of Laboratory Medicine, Eulji University School of Medicine, Seoul, Korea
| | - John Jeongseok Yang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Sung-Eun Choi
- Department of Statistics, Dongguk University, Seoul, Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
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Nath S, Shrivastava P, Kumawat RK, Dixit S, Chaubey G. Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations. Ann Hum Biol 2021; 48:360-368. [PMID: 34340604 DOI: 10.1080/03014460.2021.1957148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND India is the second most populous country in the world, which is aligned into various community segments. AIM To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study. SUBJECTS AND METHODS 15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations. RESULTS Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 105) and combined matching probability (CPm = 2.12 × 1 0 -7). CONCLUSION Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.
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Affiliation(s)
- Subhankar Nath
- DNA Typing Division, State Forensic Science Laboratory, Narsingarh, Agartala, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, India
| | - Shivani Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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Arriaga-MacKenzie IS, Matesi G, Chen S, Ronco A, Marker KM, Hall JR, Scherenberg R, Khajeh-Sharafabadi M, Wu Y, Gignoux CR, Null M, Hendricks AE. Summix: A method for detecting and adjusting for population structure in genetic summary data. Am J Hum Genet 2021; 108:1270-1282. [PMID: 34157305 PMCID: PMC8322937 DOI: 10.1016/j.ajhg.2021.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/26/2021] [Indexed: 12/11/2022] Open
Abstract
Publicly available genetic summary data have high utility in research and the clinic, including prioritizing putative causal variants, polygenic scoring, and leveraging common controls. However, summarizing individual-level data can mask population structure, resulting in confounding, reduced power, and incorrect prioritization of putative causal variants. This limits the utility of publicly available data, especially for understudied or admixed populations where additional research and resources are most needed. Although several methods exist to estimate ancestry in individual-level data, methods to estimate ancestry proportions in summary data are lacking. Here, we present Summix, a method to efficiently deconvolute ancestry and provide ancestry-adjusted allele frequencies (AFs) from summary data. Using continental reference ancestry, African (AFR), non-Finnish European (EUR), East Asian (EAS), Indigenous American (IAM), South Asian (SAS), we obtain accurate and precise estimates (within 0.1%) for all simulation scenarios. We apply Summix to gnomAD v.2.1 exome and genome groups and subgroups, finding heterogeneous continental ancestry for several groups, including African/African American (∼84% AFR, ∼14% EUR) and American/Latinx (∼4% AFR, ∼5% EAS, ∼43% EUR, ∼46% IAM). Compared to the unadjusted gnomAD AFs, Summix's ancestry-adjusted AFs more closely match respective African and Latinx reference samples. Even on modern, dense panels of summary statistics, Summix yields results in seconds, allowing for estimation of confidence intervals via block bootstrap. Given an accompanying R package, Summix increases the utility and equity of public genetic resources, empowering novel research opportunities.
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Affiliation(s)
| | - Gregory Matesi
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Samuel Chen
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Alexandria Ronco
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Katie M Marker
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jordan R Hall
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Ryan Scherenberg
- Business School, University of Colorado Denver, Denver, CO 80204, USA
| | | | - Yinfei Wu
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Christopher R Gignoux
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Megan Null
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA; Mathematics and Physical Sciences, The College of Idaho, Caldwell, ID 83605, USA
| | - Audrey E Hendricks
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA; Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA.
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