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Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M. A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment. Sci Rep 2024; 14:5583. [PMID: 38448490 PMCID: PMC10917763 DOI: 10.1038/s41598-024-56402-w] [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: 12/12/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024] Open
Abstract
In this report, we present OLAF-Seq, a novel strategy to construct a long-read sequencing library such that adjacent fragments are linked with end-terminal duplications. We use the CRISPR-Cas9 nickase enzyme and a pool of multiple sgRNAs to perform non-random fragmentation of targeted long DNA molecules (> 300kb) into smaller library-sized fragments (about 20 kbp) in a manner so as to retain physical linkage information (up to 1000 bp) between adjacent fragments. DNA molecules targeted for fragmentation are preferentially ligated with adaptors for sequencing, so this method can enrich targeted regions while taking advantage of the long-read sequencing platforms. This enables the sequencing of target regions with significantly lower total coverage, and the genome sequence within linker regions provides information for assembly and phasing. We demonstrated the validity and efficacy of the method first using phage and then by sequencing a panel of 100 full-length cancer-related genes (including both exons and introns) in the human genome. When the designed linkers contained heterozygous genetic variants, long haplotypes could be established. This sequencing strategy can be readily applied in both PacBio and Oxford Nanopore platforms for both long and short genes with an easy protocol. This economically viable approach is useful for targeted enrichment of hundreds of target genomic regions and where long no-gap contigs need deep sequencing.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Christina Huan Shi
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Danielle Piazza
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Kevin Y Yip
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA.
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Haver A, Theijn R, Grift ID, Raaijmakers G, Poorter E, Laros JFJ, van Dissel JT, Lodder WJ. Regional reemergence of a SARS-CoV-2 Delta lineage amid an Omicron wave detected by wastewater sequencing. Sci Rep 2023; 13:17870. [PMID: 37857658 PMCID: PMC10587120 DOI: 10.1038/s41598-023-44500-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 01/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
The implementation and integration of wastewater-based epidemiology constitutes a valuable addition to existing pathogen surveillance systems, such as clinical surveillance for SARS-CoV-2. In the Netherlands, SARS-CoV-2 variant circulation is monitored by performing whole-genome sequencing on wastewater samples. In this manuscript, we describe the detection of an AY.43 lineage (Delta variant) amid a period of BA.5 (Omicron variant) dominance in wastewater samples from two wastewater treatment plants (WWTPs) during the months of August and September of 2022. Our results describe a temporary emergence, which was absent in samples from other WWTPs, and which coincided with peaks in viral load. We show how these lineage estimates can be traced back to lineage-specific substitution patterns. The absence of this variant from reported clinical data, but high associated viral loads suggest cryptic transmission. Our findings highlight the additional value of wastewater surveillance for generating insights into circulating pathogens.
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Affiliation(s)
- Auke Haver
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Rick Theijn
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ivo D Grift
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gino Raaijmakers
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Elsa Poorter
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of BioInformatics and Computational Services (BIR), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jaap T van Dissel
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Benvenuto M, Palumbo P, Di Muro E, Perrotta CS, Mazza T, Mandarà GML, Palumbo O, Carella M. Identification of a Novel FOXP1 Variant in a Patient with Hypotonia, Intellectual Disability, and Severe Speech Impairment. Genes (Basel) 2023; 14:1958. [PMID: 37895307 PMCID: PMC10606110 DOI: 10.3390/genes14101958] [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: 08/04/2023] [Revised: 09/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The FOXP subfamily includes four different transcription factors: FOXP1, FOXP2, FOXP3, and FOXP4, all with important roles in regulating gene expression from early development through adulthood. Haploinsufficiency of FOXP1, due to deleterious variants (point mutations, copy number variants) disrupting the gene, leads to an emerging disorder known as "FOXP1 syndrome", mainly characterized by intellectual disability, language impairment, dysmorphic features, and multiple congenital abnormalities with or without autistic features in some affected individuals (MIM 613670). Here we describe a 10-year-old female patient, born to unrelated parents, showing hypotonia, intellectual disability, and severe language delay. Targeted resequencing analysis allowed us to identify a heterozygous de novo FOXP1 variant c.1030C>T, p.(Gln344Ter) classified as likely pathogenetic according to the American College of Medical Genetics and Genomics guidelines. To the best of our knowledge, our patient is the first to date to report carrying this stop mutation, which is, for this reason, useful for broadening the molecular spectrum of FOXP1 clinically relevant variants. In addition, our results highlight the utility of next-generation sequencing in establishing an etiological basis for heterogeneous conditions such as neurodevelopmental disorders and providing additional insight into the phenotypic features of FOXP1-related syndrome.
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Affiliation(s)
- Mario Benvenuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
- Dipartimento Degli Studi Umanistici, Università Degli Studi di Foggia, 71122 Foggia, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | - Ester Di Muro
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | | | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy;
| | | | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
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Li X, Lu K, Chen X, Tu K, Xie D. capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements. Commun Biol 2023; 6:974. [PMID: 37741908 PMCID: PMC10517987 DOI: 10.1038/s42003-023-05349-1] [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: 12/23/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression. We expect that capTEs will be a critical tool for advancing our understanding of the biological functions of individual TEs at the locus level, revealing their roles as both mutagens and regulators in biological and pathogenic processes.
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Affiliation(s)
- Xuemei Li
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Keying Lu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiao Chen
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kailing Tu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Dan Xie
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Tavernier LJM, Vanpoucke T, Schrauwen I, Van Camp G, Fransen E. Targeted Resequencing of Otosclerosis Patients from Different Populations Replicates Results from a Previous Genome-Wide Association Study. J Clin Med 2022; 11. [PMID: 36498562 DOI: 10.3390/jcm11236978] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Otosclerosis is one of the most common causes of hearing loss in young adults. It has a prevalence of 0.3-0.4% in the European population. Clinical symptoms usually occur between the second and fifth decade of life. Different studies have been performed to unravel the genetic architecture of the disease. Recently, a genome-wide association study (GWAS) identified 15 novel risk loci and replicated the regions of three previously reported candidate genes. In this study, seven candidate genes from the GWAS were resequenced using single molecule molecular inversion probes (smMIPs). smMIPs were used to capture the exonic regions and the 3' and 5' untranslated regions (UTR). Discovered variants were tested for association with the disease using single variant and gene-based association analysis. The single variant results showed that 13 significant variants were associated with otosclerosis. Associated variants were found in five of the seven genes studied here, including AHSG, LINC01482, MARK3, SUPT3H and RELN. Conversely, burden testing did not show a major role of rare variants in the disease. In conclusion, this study was able to replicate five out of seven candidate genes reported in the previous GWAS. This association is likely mainly driven by common variants.
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Yang M, Wang Y, Yin B, Zheng Q, Shi B, Jia Z. Association of soluble epoxide hydrolase 2 gene with the risk of non-syndromic cleft lip with or without cleft palate in western Han Chinese population. Hua Xi Kou Qiang Yi Xue Za Zhi 2022; 40:279-284. [PMID: 38597007 PMCID: PMC9207791 DOI: 10.7518/hxkq.2022.03.005] [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] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/20/2022] [Indexed: 04/11/2024]
Abstract
OBJECTIVES This study aimed to explore the associations between soluble epoxide hydrolase 2 gene (EPHX2) variants and non-syndromic cleft lip with or without cleft palate (NSCL/P) in Chinese Han population. METHODS We recruited 159 NSCL/P cases from Chinese Han population and carried out targeted resequencing using the whole genome sequencing data of 542 healthy Chinese individuals from Novegene internal database as controls. We classified EPHX2 variants as common or rare according to their minor allele frequency and performed an association analysis for common variations and a burden analysis for rare variations. RESULTS The lowest P-value in NSCL/P was observed at rs57699806 (P=0.000 13, OR=2.849 and 95% CI: 1.691-4.800), followed by rs4732723 (P=0.006 50, OR=0.662 and 95%CI: 0.491-0.892), rs7829267 (P=0.009 20, OR=1.496 and 95%CI: 1.117-2.005), rs721619 (P=0.011 00, OR=1.474 and 95%CI: 1.098-1.980), and rs7816586 (P=0.040 00, OR=1.310 and 95%CI: 1.015-1.691). The odds ratios suggested the C allele at rs4732723 as a protective factor for NSCL/P and the reference alleles at other single nucleotide polymorphisms (SNPs) as the risk factors for NSCL/P. Burden analysis showed no statistical significance (P>0.05). CONCLUSIONS Through targeted resequencing, this study identified five SNPs named rs57699806, rs4732723, rs7829267, rs721619, and rs7816586 around the region of EPHX2 gene associated with NSCL/P in Chinese Han population. Four SNPs of rs57699806, rs4732723, rs7829267, and rs7816586 were first identified.
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Affiliation(s)
- Mengxi Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yiru Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Bailetti D, Sentinelli F, Prudente S, Cimini FA, Barchetta I, Totaro M, Di Costanzo A, Barbonetti A, Leonetti F, Cavallo MG, Baroni MG. Deep Resequencing of 9 Candidate Genes Identifies a Role for ARAP1 and IGF2BP2 in Modulating Insulin Secretion Adjusted for Insulin Resistance in Obese Southern Europeans. Int J Mol Sci 2022; 23:ijms23031221. [PMID: 35163144 PMCID: PMC8835579 DOI: 10.3390/ijms23031221] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
Type 2 diabetes is characterized by impairment in insulin secretion, with an established genetic contribution. We aimed to evaluate common and low-frequency (1–5%) variants in nine genes strongly associated with insulin secretion by targeted sequencing in subjects selected from the extremes of insulin release measured by the disposition index. Collapsing data by gene and/or function, the association between disposition index and nonsense variants were significant, also after adjustment for confounding factors (OR = 0.25, 95% CI = 0.11–0.59, p = 0.001). Evaluating variants individually, three novel variants in ARAP1, IGF2BP2 and GCK, out of eight reaching significance singularly, remained associated after adjustment. Constructing a genetic risk model combining the effects of the three variants, only carriers of the ARAP1 and IGF2BP2 variants were significantly associated with a reduced probability to be in the lower, worst, extreme of insulin secretion (OR = 0.223, 95% CI = 0.105–0.473, p < 0.001). Observing a high number of normal glucose tolerance between carriers, a regression posthoc analysis was performed. Carriers of genetic risk model variants had higher probability to be normoglycemic, also after adjustment (OR = 2.411, 95% CI = 1.136–5.116, p = 0.022). Thus, in our southern European cohort, nonsense variants in all nine candidate genes showed association with better insulin secretion adjusted for insulin resistance, and we established the role of ARAP1 and IGF2BP2 in modulating insulin secretion.
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Affiliation(s)
- Diego Bailetti
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Correspondence: (D.B.); (M.G.B.); Tel.: +39-862-433327 (M.G.B.)
| | - Federica Sentinelli
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Sabrina Prudente
- Research Unit of Metabolic and Cardiovascular Diseases, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Flavia Agata Cimini
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Ilaria Barchetta
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Maria Totaro
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
| | - Alessia Di Costanzo
- Department of Translational and Precision Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Arcangelo Barbonetti
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
| | - Frida Leonetti
- Diabetes Unit, Department of Medical-Surgical Sciences and Biotechnologies, Santa Maria Goretti Hospital, Sapienza University of Rome, 04100 Latina, Italy;
| | - Maria Gisella Cavallo
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy; (F.A.C.); (I.B.); (M.G.C.)
| | - Marco Giorgio Baroni
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences (MeSVA), University of L’Aquila, 67100 L’Aquila, Italy; (F.S.); (M.T.); (A.B.)
- Neuroendocrinology and Metabolic Diseases, IRCCS Neuromed, 86077 Pozzilli, Italy
- Correspondence: (D.B.); (M.G.B.); Tel.: +39-862-433327 (M.G.B.)
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Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. J Genet Mutat Disord 2022; 1:103. [PMID: 35465405 PMCID: PMC9031527] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.
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Affiliation(s)
- S Polani
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - M Dean
- National Cancer Institute, Division of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics, USA
| | - A Lichter-Peled
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, USA
| | | | - X Fang
- BGI-Shenzhen, Shenzhen, China
| | - Y Feng
- BGI-Shenzhen, Shenzhen, China
| | - W Qiao
- BGI-Shenzhen, Shenzhen, China
| | - G Avni
- Medisoos Equine Clinic, Kibutz Magal, Israel
| | - G Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Iden M, Tsaih SW, Huang YW, Liu P, Xiao M, Flister MJ, Rader JS. Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br J Cancer 2021; 125:1408-19. [PMID: 34526665 DOI: 10.1038/s41416-021-01545-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/04/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Integration of human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC), yet the tumorigenicity of cis genomic changes at integration sites remains largely understudied. METHODS Combining multi-omics data from The Cancer Genome Atlas with patient-matched long-read sequencing of HPV integration sites, we developed a strategy for using HPV integration events to identify and prioritise novel candidate ICC target genes (integration-detected genes (IDGs)). Four IDGs were then chosen for in vitro functional studies employing small interfering RNA-mediated knockdown in cell migration, proliferation and colony formation assays. RESULTS PacBio data revealed 267 unique human-HPV breakpoints comprising 87 total integration events in eight tumours. Candidate IDGs were filtered based on the following criteria: (1) proximity to integration site, (2) clonal representation of integration event, (3) tumour-specific expression (Z-score) and (4) association with ICC survival. Four candidates prioritised based on their unknown function in ICC (BNC1, RSBN1, USP36 and TAOK3) exhibited oncogenic properties in cervical cancer cell lines. Further, annotation of integration events provided clues regarding potential mechanisms underlying altered IDG expression in both integrated and non-integrated ICC tumours. CONCLUSIONS HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.
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Dilliott AA, Abdelhady A, Sunderland KM, Farhan SMK, Abrahao A, Binns MA, Black SE, Borrie M, Casaubon LK, Dowlatshahi D, Finger E, Fischer CE, Frank A, Freedman M, Grimes D, Hassan A, Jog M, Kumar S, Kwan D, Lang AE, Mandzia J, Masellis M, McIntyre AD, Pasternak SH, Pollock BG, Rajji TK, Rogaeva E, Sahlas DJ, Saposnik G, Sato C, Seitz D, Shoesmith C, Steeves TDL, Swartz RH, Tan B, Tang-Wai DF, Tartaglia MC, Turnbull J, Zinman L, Hegele RA. Contribution of rare variant associations to neurodegenerative disease presentation. NPJ Genom Med 2021; 6:80. [PMID: 34584092 PMCID: PMC8478934 DOI: 10.1038/s41525-021-00243-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
Genetic factors contribute to neurodegenerative diseases, with high heritability estimates across diagnoses; however, a large portion of the genetic influence remains poorly understood. Many previous studies have attempted to fill the gaps by performing linkage analyses and association studies in individual disease cohorts, but have failed to consider the clinical and pathological overlap observed across neurodegenerative diseases and the potential for genetic overlap between the phenotypes. Here, we leveraged rare variant association analyses (RVAAs) to elucidate the genetic overlap among multiple neurodegenerative diagnoses, including Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia (FTD), mild cognitive impairment, and Parkinson's disease (PD), as well as cerebrovascular disease, using the data generated with a custom-designed neurodegenerative disease gene panel in the Ontario Neurodegenerative Disease Research Initiative (ONDRI). As expected, only ~3% of ONDRI participants harboured a monogenic variant likely driving their disease presentation. Yet, when genes were binned based on previous disease associations, we observed an enrichment of putative loss of function variants in PD genes across all ONDRI cohorts. Further, individual gene-based RVAA identified significant enrichment of rare, nonsynonymous variants in PARK2 in the FTD cohort, and in NOTCH3 in the PD cohort. The results indicate that there may be greater heterogeneity in the genetic factors contributing to neurodegeneration than previously appreciated. Although the mechanisms by which these genes contribute to disease presentation must be further explored, we hypothesize they may be a result of rare variants of moderate phenotypic effect contributing to overlapping pathology and clinical features observed across neurodegenerative diagnoses.
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Affiliation(s)
- Allison A Dilliott
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
| | - Abdalla Abdelhady
- Department of Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Kelly M Sunderland
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
| | - Sali M K Farhan
- Departments of Neurology and Neurosurgery, and Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Agessandro Abrahao
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre and University of Toronto, Toronto, ON, Canada
| | - Malcolm A Binns
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Sandra E Black
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre and University of Toronto, Toronto, ON, Canada
- LCCampbell Cognitive Neurology Research Unit, Hurvitz Brain Sciences Research Program Sunnybrook Health Sciences Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Michael Borrie
- St. Joseph's Health Care Centre, London, ON, Canada
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Leanne K Casaubon
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
- University Health Network Stroke Program, Toronto Western Hospital, Toronto, ON, Canada
| | - Dar Dowlatshahi
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Elizabeth Finger
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
| | - Corinne E Fischer
- Keenan Research Centre for Biomedical Research, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Andrew Frank
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- Bruyère Research Institute, Ottawa, ON, Canada
| | - Morris Freedman
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, Baycrest Health Sciences, Mt. Sinai Hospital and University of Toronto, Toronto, ON, Canada
| | - David Grimes
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Ayman Hassan
- Thunder Bay Regional Research Institute and Northern Ontario School of Medicine, Thunder Bay, ON, Canada
| | - Mandar Jog
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Health Sciences Centre, London, ON, Canada
| | - Sanjeev Kumar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Donna Kwan
- Centre for Neuroscience Studies, Queen's University, Kingston, ON, Canada
| | - Anthony E Lang
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON, Canada
| | - Jennifer Mandzia
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Mario Masellis
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
- Cognitive & Movement Disorders Clinic and L.C. Campbell Cognitive Neurology Research Unit, Hurvitz Brain Science Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Stephen H Pasternak
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Cognitive Neurology and Alzheimer's Disease Research Centre, Parkwood Institute, St. Joseph's Health Care, London, ON, Canada
| | - Bruce G Pollock
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tarek K Rajji
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry and Toronto Dementia Research Alliance, University of Toronto, Toronto, ON, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Gustavo Saposnik
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- Clinical Outcomes and Decision Neuroscience Unit, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Dallas Seitz
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Thomas D L Steeves
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
- Division of Neurology, St. Michael's Hospital, Toronto, ON, Canada
| | - Richard H Swartz
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre and University of Toronto, Toronto, ON, Canada
- LCCampbell Cognitive Neurology Research Unit, Hurvitz Brain Sciences Research Program Sunnybrook Health Sciences Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
| | - Brian Tan
- Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
| | - David F Tang-Wai
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, Toronto Western Hospital, Toronto, ON, Canada
- University Health Network Memory Clinic, Toronto Western Hospital, Toronto, ON, Canada
| | - Maria C Tartaglia
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - John Turnbull
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Lorne Zinman
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre and University of Toronto, Toronto, ON, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
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11
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Aamer W, Hassan HY, Nakaoka H, Hosomichi K, Jaeger M, Tahir H, Abdelraheem MH, Netea MG, Inoue I. Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan. Eur J Hum Genet 2021; 29:1259-71. [PMID: 33753913 DOI: 10.1038/s41431-021-00845-6] [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] [Received: 06/27/2020] [Revised: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.
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12
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Numaguchi K, Akagi T, Kitamura Y, Ishikawa R, Ishii T. Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume). Plant J 2020; 104:1551-1567. [PMID: 33048374 DOI: 10.1111/tpj.15020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 07/12/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.
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Affiliation(s)
- Koji Numaguchi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, Minabe, Higashi-honjo 1416-7, Wakayama, 645-0021, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Tsushima-naka 1-1-1, Okayama, 700-8530, Japan
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, Minabe, Higashi-honjo 1416-7, Wakayama, 645-0021, Japan
| | - Ryo Ishikawa
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
| | - Takashige Ishii
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
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13
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Kulkarni R, Chopra R, Chagoya J, Simpson CE, Baring MR, Hillhouse A, Puppala N, Chamberlin K, Burow MD. Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes. Genes (Basel) 2020; 11:E1220. [PMID: 33080972 DOI: 10.3390/genes11101220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Received: 09/08/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 11/18/2022] Open
Abstract
The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.
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14
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Mego M, Karaba M, Sedlackova T, Benca J, Repiska G, Krasnicanova L, Macuch J, Sieberova G, Jurisova S, Pindak D, Kalavska K, Mardiak J, Minarik G. Circulating tumor cells and breast cancer-specific mutations in primary breast cancer. Mol Clin Oncol 2020; 12:565-573. [PMID: 32337039 DOI: 10.3892/mco.2020.2026] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 01/29/2020] [Indexed: 12/29/2022] Open
Abstract
Circulating tumor cells (CTCs) play a pivotal role in tumor dissemination and progression, and are considered to be a critical part of the metastatic cascade. The aim of the present research article was to examine breast cancer-specific mutations in primary breast cancer (PBC) using targeted resequencing. A total of 78 patients with PBC were enrolled into this translational study. Reverse transcription-quantitative PCR assay for the expression of epithelial markers (CK19) or epithelial-to-mesenchymal transition (EMT)-related genes (TWIST1, SNAIL1, SLUG and ZEB1) was applied for identification of CTCs prior to surgery. Total DNA was isolated from fresh frozen primary tumors. Sequencing was performed by Agilent SureSelect target enrichment and Illumina paired-end sequencing on the MiSeq platform. The most commonly affected genes were TP53 (mutated in 21 tumors; 26.9%), followed by PIK3CA (mutated in 16 tumors; 20.5%) and BRCA1/2 (mutated in 7 tumors, BRCA1 n=2 and BRCA2 n=5; 9.0%). In our cohort, a significantly higher proportion of patients with epithelial CTCs harbored mutations in the BRCA1/2 genes in the tumor tissue. There were no mutations in specific genes associated with CTCs with the EMT phenotype. To the best of our knowledge, this study is the first to report a correlation between the presence of epithelial CTCs in the peripheral blood and mutations of the BRCA1/2 genes in primary tumor tissue.
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Affiliation(s)
- Michal Mego
- Second Department of Medical Oncology, Faculty of Medicine, Comenius University, 833 10 Bratislava, Slovakia.,National Cancer Institute, 833 10 Bratislava, Slovakia
| | - Marian Karaba
- National Cancer Institute, 833 10 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Juraj Benca
- National Cancer Institute, 833 10 Bratislava, Slovakia.,Department of Medicine, St. Elizabeth University, 811 02 Bratislava, Slovakia
| | - Gabriela Repiska
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Lucia Krasnicanova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jan Macuch
- National Cancer Institute, 833 10 Bratislava, Slovakia
| | | | - Silvia Jurisova
- Second Department of Medical Oncology, Faculty of Medicine, Comenius University, 833 10 Bratislava, Slovakia.,National Cancer Institute, 833 10 Bratislava, Slovakia
| | - Daniel Pindak
- National Cancer Institute, 833 10 Bratislava, Slovakia.,Slovak Medical University, 833 03 Bratislava, Slovakia
| | - Katarina Kalavska
- Second Department of Medical Oncology, Faculty of Medicine, Comenius University, 833 10 Bratislava, Slovakia.,National Cancer Institute, 833 10 Bratislava, Slovakia
| | - Jozef Mardiak
- Second Department of Medical Oncology, Faculty of Medicine, Comenius University, 833 10 Bratislava, Slovakia.,National Cancer Institute, 833 10 Bratislava, Slovakia
| | - Gabriel Minarik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina, 842 15 Bratislava, Slovakia
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15
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Moore C, Blumhagen RZ, Yang IV, Walts A, Powers J, Walker T, Bishop M, Russell P, Vestal B, Cardwell J, Markin CR, Mathai SK, Schwarz MI, Steele MP, Lee J, Brown KK, Loyd JE, Crapo JD, Silverman EK, Cho MH, James JA, Guthridge JM, Cogan JD, Kropski JA, Swigris JJ, Bair C, Kim DS, Ji W, Kim H, Song JW, Maier LA, Pacheco KA, Hirani N, Poon AS, Li F, Jenkins RG, Braybrooke R, Saini G, Maher TM, Molyneaux PL, Saunders P, Zhang Y, Gibson KF, Kass DJ, Rojas M, Sembrat J, Wolters PJ, Collard HR, Sundy JS, O’Riordan T, Strek ME, Noth I, Ma SF, Porteous MK, Kreider ME, Patel NB, Inoue Y, Hirose M, Arai T, Akagawa S, Eickelberg O, Fernandez IE, Behr J, Mogulkoc N, Corte TJ, Glaspole I, Tomassetti S, Ravaglia C, Poletti V, Crestani B, Borie R, Kannengiesser C, Parfrey H, Fiddler C, Rassl D, Molina-Molina M, Machahua C, Worboys AM, Gudmundsson G, Isaksson HJ, Lederer DJ, Podolanczuk AJ, Montesi SB, Bendstrup E, Danchel V, Selman M, Pardo A, Henry MT, Keane MP, Doran P, Vašáková M, Sterclova M, Ryerson CJ, Wilcox PG, Okamoto T, Furusawa H, Miyazaki Y, Laurent G, Baltic S, Prele C, Moodley Y, Shea BS, Ohta K, Suzukawa M, Narumoto O, Nathan SD, Venuto DC, Woldehanna ML, Kokturk N, de Andrade JA, Luckhardt T, Kulkarni T, Bonella F, Donnelly SC, McElroy A, Armstong ME, Aranda A, Carbone RG, Puppo F, Beckman KB, Nickerson DA, Fingerlin TE, Schwartz DA. Resequencing Study Confirms That Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 200:199-208. [PMID: 31034279 PMCID: PMC6635791 DOI: 10.1164/rccm.201810-1891oc] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [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: 10/08/2018] [Accepted: 04/22/2019] [Indexed: 12/20/2022] Open
Abstract
Rationale: Several common and rare genetic variants have been associated with idiopathic pulmonary fibrosis, a progressive fibrotic condition that is localized to the lung. Objectives: To develop an integrated understanding of the rare and common variants located in multiple loci that have been reported to contribute to the risk of disease. Methods: We performed deep targeted resequencing (3.69 Mb of DNA) in cases (n = 3,624) and control subjects (n = 4,442) across genes and regions previously associated with disease. We tested for associations between disease and 1) individual common variants via logistic regression and 2) groups of rare variants via sequence kernel association tests. Measurements and Main Results: Statistically significant common variant association signals occurred in all 10 of the regions chosen based on genome-wide association studies. The strongest risk variant is the MUC5B promoter variant rs35705950, with an odds ratio of 5.45 (95% confidence interval, 4.91-6.06) for one copy of the risk allele and 18.68 (95% confidence interval, 13.34-26.17) for two copies of the risk allele (P = 9.60 × 10-295). In addition to identifying for the first time that rare variation in FAM13A is associated with disease, we confirmed the role of rare variation in the TERT and RTEL1 gene regions in the risk of IPF, and found that the FAM13A and TERT regions have independent common and rare variant signals. Conclusions: A limited number of common and rare variants contribute to the risk of idiopathic pulmonary fibrosis in each of the resequencing regions, and these genetic variants focus on biological mechanisms of host defense and cell senescence.
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Affiliation(s)
- Camille Moore
- National Jewish Health, Denver, Colorado
- School of Public Health
| | | | | | | | | | | | | | | | | | | | - Cheryl R. Markin
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | | | | | - James E. Loyd
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James D. Crapo
- National Jewish Health, Denver, Colorado
- Department of Medicine, and
| | - Edwin K. Silverman
- Brigham and Women’s Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Michael H. Cho
- Brigham and Women’s Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Judith A. James
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | | | - Joy D. Cogan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jonathan A. Kropski
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Carol Bair
- National Jewish Health, Denver, Colorado
| | - Dong Soon Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Wonjun Ji
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hocheol Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Woo Song
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Lisa A. Maier
- National Jewish Health, Denver, Colorado
- School of Public Health
- Department of Medicine, and
| | | | - Nikhil Hirani
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- Respiratory Medicine Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Azin S. Poon
- Respiratory Medicine Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Feng Li
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - R. Gisli Jenkins
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Braybrooke
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gauri Saini
- Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Toby M. Maher
- Royal Brompton Hospital and Imperial College, London, United Kingdom
| | | | - Peter Saunders
- Royal Brompton Hospital and Imperial College, London, United Kingdom
| | - Yingze Zhang
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kevin F. Gibson
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel J. Kass
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mauricio Rojas
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John Sembrat
- Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Harold R. Collard
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | | | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Mary K. Porteous
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maryl E. Kreider
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Namrata B. Patel
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yoshikazu Inoue
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Masaki Hirose
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Toru Arai
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Shinobu Akagawa
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Oliver Eickelberg
- Department of Medicine, and
- Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Nesrin Mogulkoc
- Department of Pulmonology, Ege University Hospital, Bornova, Izmir, Turkey
| | - Tamera J. Corte
- Royal Prince Alfred Hospital and University of Sydney, Sydney, Australia
| | - Ian Glaspole
- Alfred Hospital and Monash University, Melbourne, Australia
| | | | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Bruno Crestani
- Université Paris Diderot and Hôpital Bichat, Paris, France
| | - Raphael Borie
- Université Paris Diderot and Hôpital Bichat, Paris, France
| | | | - Helen Parfrey
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Christine Fiddler
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Doris Rassl
- Royal Papworth Hospital and Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Maria Molina-Molina
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Carlos Machahua
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Ana Montes Worboys
- Respiratory Department, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | - Gunnar Gudmundsson
- National University Hospital of Iceland, University of Iceland, Reykjavik, Iceland
| | - Helgi J. Isaksson
- National University Hospital of Iceland, University of Iceland, Reykjavik, Iceland
| | - David J. Lederer
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Anna J. Podolanczuk
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Elisabeth Bendstrup
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | - Vivi Danchel
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas,” México City, México
| | - Annie Pardo
- Universidad Nacional Autónoma de México, México City, México
| | - Michael T. Henry
- Cork University Hospital and University College Cork, Cork, Ireland
| | - Michael P. Keane
- St. Vincent’s University Hospital, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Peter Doran
- St. Vincent’s University Hospital, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Martina Vašáková
- Department of Respiratory Medicine, First Faculty of Medicine Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Martina Sterclova
- Department of Respiratory Medicine, First Faculty of Medicine Charles University and Thomayer Hospital, Prague, Czech Republic
| | | | | | - Tsukasa Okamoto
- Department of Medicine, and
- Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruhiko Furusawa
- Department of Medicine, and
- Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Geoffrey Laurent
- Institute for Respiratory Health and
- Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | | | - Cecilia Prele
- Institute for Respiratory Health and
- Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | | | - Barry S. Shea
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Ken Ohta
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Maho Suzukawa
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Osamu Narumoto
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Steven D. Nathan
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Drew C. Venuto
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Merte L. Woldehanna
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia
| | - Nurdan Kokturk
- Department of Pulmonary Medicine, Gazi University School of Medicine, Ankara, Turkey
| | - Joao A. de Andrade
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tracy Luckhardt
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tejaswini Kulkarni
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Francesco Bonella
- Ruhrlandklinik, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Seamus C. Donnelly
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Aoife McElroy
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Michelle E. Armstong
- Department of Medicine, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Alvaro Aranda
- CardioPulmonary Reserach Center, Alliance Pulmonary Group, Guaynabo, Puerto Rico
| | | | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Kenneth B. Beckman
- Biomedical Genomics Center, University of Minnesota; Minneapolis, Minnesota; and
| | | | - Tasha E. Fingerlin
- National Jewish Health, Denver, Colorado
- School of Public Health
- Department of Medicine, and
| | - David A. Schwartz
- National Jewish Health, Denver, Colorado
- Department of Medicine, and
- Department of Immunology, University of Colorado Denver, Denver, Colorado
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16
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Zhou WZ, Zhang J, Li Z, Lin X, Li J, Wang S, Yang C, Wu Q, Ye AY, Wang M, Wang D, Pu TZ, Wu YY, Wei L. Targeted resequencing of 358 candidate genes for autism spectrum disorder in a Chinese cohort reveals diagnostic potential and genotype-phenotype correlations. Hum Mutat 2019; 40:801-815. [PMID: 30763456 PMCID: PMC6593842 DOI: 10.1002/humu.23724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 08/23/2018] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 12/30/2022]
Abstract
Autism spectrum disorder (ASD) is a childhood neuropsychiatric disorder with a complex genetic architecture. The diagnostic potential of a targeted panel of ASD genes has only been evaluated in small cohorts to date and is especially understudied in the Chinese population. Here, we designed a capture panel with 358 genes (111 syndromic and 247 nonsyndromic) for ASD and sequenced a Chinese cohort of 539 cases evaluated with the Autism Diagnostic Interview‐Revised (ADI‐R) and the Autism Diagnostic Observation Schedule (ADOS) as well as 512 controls. ASD cases were found to carry significantly more ultra‐rare functional variants than controls. A subset of 78 syndromic and 54 nonsyndromic genes was the most significantly associated and should be given high priority in the future screening of ASD patients. Pathogenic and likely pathogenic variants were detected in 9.5% of cases. Variants in SHANK3 and SHANK2 were the most frequent, especially in females, and occurred in 1.2% of cases. Duplications of 15q11–13 were detected in 0.8% of cases. Variants in CNTNAP2 and MEF2C were correlated with epilepsy/tics in cases. Our findings reveal the diagnostic potential of ASD genetic panel testing and new insights regarding the variant spectrum. Genotype–phenotype correlations may facilitate the diagnosis and management of ASD.
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Affiliation(s)
- Wei-Zhen Zhou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Zhang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ziyi Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaojing Lin
- National Institute of Biological Sciences, Beijing, China
| | - Jiarui Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Changhong Yang
- National Institute of Biological Sciences, Beijing, China.,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qixi Wu
- School of Life Sciences, Peking University, Beijing, China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Meng Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Dandan Wang
- National Institute of Biological Sciences, Beijing, China
| | | | - Yu-Yu Wu
- Yuning Psychiatry Clinic, Taipei, Taiwan
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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17
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Veeckman E, Van Glabeke S, Haegeman A, Muylle H, van Parijs FRD, Byrne SL, Asp T, Studer B, Rohde A, Roldán-Ruiz I, Vandepoele K, Ruttink T. Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne). DNA Res 2019; 26:1-12. [PMID: 30325414 PMCID: PMC6379033 DOI: 10.1093/dnares/dsy033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/26/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.
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Affiliation(s)
- Elisabeth Veeckman
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium
| | | | | | | | | | | | - Torben Asp
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Center Flakkebjerg Aarhus University, DK Slagelse, Denmark
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, CH Zurich, Switzerland
| | | | - Isabel Roldán-Ruiz
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium
| | - Klaas Vandepoele
- Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B Ghent, Belgium.,Center for Plant Systems Biology, VIB, B Ghent, Belgium
| | - Tom Ruttink
- ILVO, Plant Sciences Unit, B Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, B Ghent, Belgium
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18
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Abstract
Schizophrenia is a highly heritable psychiatric disorder that affects 1% of the population. Genome-wide association studies have identified common variants in candidate genes associated with schizophrenia, but the genetics mechanisms of this disorder have not yet been elucidated. The discovery of rare genetic variants that contribute to schizophrenia symptoms promises to help explain the missing heritability of the disease. Next generation sequencing techniques are revolutionizing the field of psychiatric genetics. Various statistical approaches have been developed for rare variant association testing in case-control and family studies. Targeted resequencing, whole exome sequencing and whole genome sequencing combined with these computational tools are used for the discovery of rare genetic variations in schizophrenia. The findings provide useful information for characterizing the rare mutations and elucidating the genetic mechanisms by which the variants cause schizophrenia.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Fatimah Jackson
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC 20059, USA
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19
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Kimura Y, Akahira-Azuma M, Harada N, Enomoto Y, Tsurusaki Y, Kurosawa K. Novel SYNGAP1 variant in a patient with intellectual disability and distinctive dysmorphisms. Congenit Anom (Kyoto) 2018; 58:188-190. [PMID: 29381230 DOI: 10.1111/cga.12273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 11/27/2022]
Abstract
We describe a novel de novo heterozygous variant in SYNGAP1 (c.1741C>T, p.R581W), identified through targeted resequencing in an 8-year-old boy with intellectual disability, autism spectrum disorder, distinctive dysmorphic features, and no seizures. Our data strongly suggest that the SYNGAP1 variant is causative of intellectual disability in this patient.
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Affiliation(s)
- Yuichi Kimura
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Moe Akahira-Azuma
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriaki Harada
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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20
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Tsai MH, Chan CK, Chang YC, Lin CH, Liou CW, Chang WN, Ng CC, Lim KS, Hwang DY. Molecular Genetic Characterization of Patients With Focal Epilepsy Using a Customized Targeted Resequencing Gene Panel. Front Neurol 2018; 9:515. [PMID: 30034362 PMCID: PMC6043663 DOI: 10.3389/fneur.2018.00515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/08/2018] [Accepted: 06/11/2018] [Indexed: 12/30/2022] Open
Abstract
Objective: Focal epilepsy is the most common subtype of epilepsies in which the influence of underlying genetic factors is emerging but remains largely uncharacterized. The purpose of this study is to determine the contribution of currently known disease-causing genes in a large cohort (n = 593) of common focal non-lesional epilepsy patients. Methods: The customized focal epilepsy gene panel (21 genes) was based on multiplex polymerase chain reaction (PCR) and sequenced by Illumina MiSeq platform. Results: Eleven variants (1.85%) were considered as pathogenic or likely pathogenic, including seven novel mutations. There were three SCN1A (p.Leu890Pro, p.Arg1636Ter, and p.Met1714Val), three PRRT2 (two p.Arg217Profs*8 and p.Leu298Pro), two CHRNA4 (p.Ser284Leu, p.Ile321Asn), one DEPDC5 (p.Val516Ter), one PCDH19 (p.Asp233Asn), and one SLC2A1 (p.Ser414Ter) variants. Additionally, 16 other rare variants were classified as unknown significance due to inconsistent phenotype or lack of segregation data. Conclusion: Currently known focal epilepsy genes only explained a very small subset of focal epilepsy patients. This indicates that the underlying genetic architecture of focal epilepsies is very heterogeneous and more novel genes are likely to be discovered. Our study highlights the usefulness, challenges and limitations of using the multi-gene panel as a diagnostic test in routine clinical practice in patients with focal epilepsy.
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Affiliation(s)
- Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Chung-Kin Chan
- Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Ying-Chao Chang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chih-Hsiang Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Wen-Neng Chang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Ching-Ching Ng
- Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Kheng-Seang Lim
- Division of Neurology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Daw-Yang Hwang
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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21
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Yoshihama T, Fukunaga K, Hirasawa A, Nomura H, Akahane T, Kataoka F, Yamagami W, Aoki D, Mushiroda T. GSTP1 rs1695 is associated with both hematological toxicity and prognosis of ovarian cancer treated with paclitaxel plus carboplatin combination chemotherapy: a comprehensive analysis using targeted resequencing of 100 pharmacogenes. Oncotarget 2018; 9:29789-29800. [PMID: 30038720 PMCID: PMC6049855 DOI: 10.18632/oncotarget.25712] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 04/07/2018] [Accepted: 06/13/2018] [Indexed: 01/08/2023] Open
Abstract
Purpose To find genetic variants that predicted toxicity and/or efficacy of paclitaxel plus carboplatin combination therapy (TC therapy). Patients and methods In a retrospective case-control study, we analyzed 320 patients who had received TC therapy for gynecological cancers (ovarian, fallopian tube, peritoneal, uterine, and cervical cancers) and collected their germline DNA. We performed a comprehensive pharmacogenomic analysis using a targeted resequencing panel of 100 pharmacogenes. For 1,013 variants passing QC, case-control association studies and survival analyses were conducted. Results GSTP1 rs1695 showed the smallest p value for hematotoxicity association, and the 105Ile wild type allele had a significantly higher risk of severe hematotoxicity (neutropenia G4, thrombocytopenia ≥ G3 and anemia ≥ G3) than the 105Val allele (p=0.00034, odds ratio=5.71 (95% confidence interval:1.77-18.44)). Next, we assessed 5-year progression-free survival (PFS) and overall survival (OS) in 56 advanced ovarian cancer patients who received tri-weekly TC as a first-line chemotherapy. Patients with the 105Ile/105Ile genotype showed significantly better PFS (p=0.00070) and OS (p=0.0012) than those with the 105Ile/105Val or 105Val/105Val genotype. Conclusion Our study indicates that the GSTP1 rs1695 105Ile/105Ile genotype is associated with both severe hematotoxicity and high efficacy of TC therapy, identifying a possible prognostic indicator for patients with TC therapy.
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Affiliation(s)
- Tomoko Yoshihama
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akira Hirasawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Nomura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Akahane
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Fumio Kataoka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Yamagami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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22
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Pankin A, Altmüller J, Becker C, von Korff M. Targeted resequencing reveals genomic signatures of barley domestication. New Phytol 2018; 218:1247-1259. [PMID: 29528492 PMCID: PMC5947139 DOI: 10.1111/nph.15077] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 08/23/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.
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Affiliation(s)
- Artem Pankin
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Christian Becker
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Maria von Korff
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’Heinrich‐Heine‐University40225DüsseldorfGermany
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23
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Kim BJ, Kim AR, Han JH, Lee C, Oh DY, Choi BY. Discovery of MYH14 as an important and unique deafness gene causing prelingually severe autosomal dominant nonsyndromic hearing loss. J Gene Med 2017; 19. [PMID: 28221712 DOI: 10.1002/jgm.2950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 12/15/2016] [Revised: 02/04/2017] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Pathogenic variants of MYH14 are known to be associated (in either a syndromic or nonsyndromic manner) with hearing loss. Interestingly, all reported cases to date of MYH14-related nonsyndromic hearing loss with detailed phenotypes have demonstrated mild-to-moderate progressive hearing loss with postlingual onset. METHODS In the present study, targeted resequencing (TRS) of known deafness genes was performed to identify the causative variant in two multiplex families segregating autosomal dominant (AD) inherited hearing loss. RESULTS TRS uncovered two novel variants of MYH14 (c.A572G: p.Asp191Gly in the myosin head domain and c.C73T:p.Gln25* in exon 2) from two multiplex deafness Korean families. Notably, both probands showed phenotypes of congenital or prelingual severe hearing loss. It is remarkably uncommon to encounter such a severe-to-profound, prelingual, AD hearing loss. Given that the first variant, p. Asp191Gly, was the first documented missense allele discovered in the myosin head domain of this gene related to either congenital or prelingual severe nonsyndromic hearing loss, and also that the second variant, p. Gln25*, lead to a null allele, more severe phenotypes from our probands may have been the result of either genotype-phenotype correlation or genetic backgrounds, or both. CONCLUSIONS In the present study, we report that MYH14 can manifest as nonsyndromic prelingual severe sensorineural hearing loss in an AD fashion in Koreans. The results of the present study suggest that further genetic studies of similar patients should consider MYH14 as a causative gene, and cochlear implantation during infant or early childhood should be indicated for those patients with certain MYH14 pathogenic variants.
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Affiliation(s)
- Bong Jik Kim
- Wide River Institute of Immunology, Seoul National University College of Medicine, Seoul, South Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
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24
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Abstract
Our earlier genome-wide linkage study of body mass index (BMI) showed strong signals from 7q36.3 and 8q21.13. This case-control study set to investigate 2 genomic regions which may harbor variants contributed to development of obesity.We employed targeted resequencing technology to detect single nucleotide polymorphisms (SNPs) in 7q36.3 and 8q21.13 from 16 individuals with obesity. These were compared with 504 East Asians in the 1000 Genomes Project as a reference panel. Linkage disequilibrium (LD) block analysis was performed for the significant SNPs located near the same gene. Genes involved in statistically significant loci were then subject to gene set enrichment analysis (GSEA).The 16 individuals aged between 30 and 60 years with BMI = 33.25 ± 2.22 kg/m. A total of 12,131 genetic variants across all of samples were found. After correcting for multiple testing, 65 SNPs from 25 nearest genes (INSIG1, FABP5, PTPRN2, VIPR2, WDR60, SHH, UBE3C, LMBR1, PAG1, IMPA1, CHMP4, SNX16, BLACE, EN2, CNPY1, LOC100506302, RBM33, LOC389602, LOC285889, LINC01006, NOM1, DNAJB6, LOC101927914, ESYT2, LINC00689) were associated with obesity at significant level q-value ≤ 0.05. LD block analysis showed there were 10 pairs of loci with D' ≥ 0.8 and r ≥ 0.8. GSEA further identified 2 major related gene sets, involving lipid raft and lipid metabolic process, with FDR values <0.12 and <0.4, respectively.Our data are the first documentation of genetic variants in 7q36.3 and 8q21.13 associated with obesity using target capture sequencing and Northern Han Chinese samples. Additional replication and functional studies are merited to validate our findings.
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25
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Manzoli GN, Bademci G, Acosta AX, Félix TM, Cengiz FB, Foster J, Da Silva DSD, Menendez I, Sanchez-Pena I, Tekin D, Blanton SH, Abe-Sandes K, Liu XZ, Tekin M. Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil. Ann Hum Genet 2016; 80:327-331. [PMID: 27870113 PMCID: PMC5127167 DOI: 10.1111/ahg.12177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 03/07/2016] [Revised: 08/23/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.
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Affiliation(s)
- Gabrielle N Manzoli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Angelina X Acosta
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Têmis M Félix
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre, Brazil
| | - F Basak Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Joseph Foster
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Danniel S Dias Da Silva
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Ibis Menendez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Isalis Sanchez-Pena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Kiyoko Abe-Sandes
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Xue Zhong Liu
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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26
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Eyres I, Duvaux L, Gharbi K, Tucker R, Hopkins D, Simon JC, Ferrari J, Smadja CM, Butlin RK. Targeted re-sequencing confirms the importance of chemosensory genes in aphid host race differentiation. Mol Ecol 2016; 26:43-58. [PMID: 27552184 PMCID: PMC6849616 DOI: 10.1111/mec.13818] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 02/02/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023]
Abstract
Host‐associated races of phytophagous insects provide a model for understanding how adaptation to a new environment can lead to reproductive isolation and speciation, ultimately enabling us to connect barriers to gene flow to adaptive causes of divergence. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on legume species and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. As host choice produces assortative mating, understanding the underlying mechanisms of choice will contribute directly to understanding of speciation. As host choice in the pea aphid is likely mediated by smell and taste, we use capture sequencing and SNP genotyping to test for the role of chemosensory genes in the divergence between eight host plant species across the continuum of differentiation and sampled at multiple locations across western Europe. We show high differentiation of chemosensory loci relative to control loci in a broad set of pea aphid races and localities, using a model‐free approach based on principal component analysis. Olfactory and gustatory receptors form the majority of highly differentiated genes and include loci that were already identified as outliers in a previous study focusing on the three most closely related host races. Consistent indications that chemosensory genes may be good candidates for local adaptation and barriers to gene flow in the pea aphid open the way to further investigations aiming to understand their impact on gene flow and to determine their precise functions in response to host plant metabolites.
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Affiliation(s)
- Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3JT, Edinburgh, UK
| | - Rachel Tucker
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - David Hopkins
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Jean-Christophe Simon
- Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, INRA, 35653, Le Rheu Cedex, France
| | - Julia Ferrari
- Department of Biology, University of York, York YO10 5DD, UK
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS-IRD-CIRAD-Université de Montpellier), Université de Montpellier, cc065, Place Bataillon, Campus Triolet, 34095, Montpellier Cedex 05, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
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27
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Barresi S, Niceta M, Alfieri P, Brankovic V, Piccini G, Bruselles A, Barone MR, Cusmai R, Tartaglia M, Bertini E, Zanni G. Mutations in the IRBIT domain of ITPR1 are a frequent cause of autosomal dominant nonprogressive congenital ataxia. Clin Genet 2016; 91:86-91. [PMID: 27062503 DOI: 10.1111/cge.12783] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 01/23/2023]
Abstract
Congenital ataxias are nonprogressive neurological disorders characterized by neonatal hypotonia, developmental delay and ataxia, variably associated with intellectual disability and other neurological or extraneurological features. We performed trio-based whole-exome sequencing of 12 families with congenital cerebellar and/or vermis atrophy in parallel with targeted next-generation sequencing of known ataxia genes (CACNA1A, ITPR1, KCNC3, ATP2B3 and GRM1) in 12 additional patients with a similar phenotype. Novel pathological mutations of ITPR1 (inositol 1,4,5-trisphosphate receptor, type 1) were found in seven patients from four families (4/24, ∼16.8%) all localized in the IRBIT (inositol triphosphate receptor binding protein) domain which plays an essential role in the regulation of neuronal plasticity and development. Our study expands the mutational spectrum of ITPR1-related congenital ataxia and indicates that ITPR1 gene screening should be implemented in this subgroup of ataxias.
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Affiliation(s)
- S Barresi
- Department of Neurosciences, Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - M Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - P Alfieri
- Department of Neurosciences, Child Neuropsychiatry, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - V Brankovic
- Clinic for Child Neurology and Psychiatry, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - G Piccini
- Department of Neurosciences, Child Neuropsychiatry, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - A Bruselles
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - M R Barone
- Centro ambulatoriale di Riabilitazione, Fondazione Betania Onlus, Catanzaro, Italy
| | - R Cusmai
- Department of Neurosciences, Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - M Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - E Bertini
- Department of Neurosciences, Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - G Zanni
- Department of Neurosciences, Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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28
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Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, Boudewyns A, De Leenheer E, Janssens S, Claes K, Verstreken M, Strenzke N, Predöhl F, Wuyts W, Mortier G, Bitner-Glindzicz M, Moser T, Coucke P, Huentelman MJ, Van Camp G. DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System. Hum Mutat 2016; 37:812-9. [PMID: 27068579 DOI: 10.1002/humu.22999] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 07/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
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Affiliation(s)
- Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jenneke van den Ende
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Els De Leenheer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Margriet Verstreken
- University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium
| | - Nicola Strenzke
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Friederike Predöhl
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Maria Bitner-Glindzicz
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Tobias Moser
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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29
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Khermesh K, D'Erchia AM, Barak M, Annese A, Wachtel C, Levanon EY, Picardi E, Eisenberg E. Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease. RNA 2016; 22:290-302. [PMID: 26655226 PMCID: PMC4712678 DOI: 10.1261/rna.054627.115] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/18/2015] [Indexed: 05/20/2023]
Abstract
Adenosine to inosine (A-to-I) RNA editing, catalyzed by the ADAR enzyme family, acts on dsRNA structures within pre-mRNA molecules. Editing of the coding part of the mRNA may lead to recoding, amino acid substitution in the resulting protein, possibly modifying its biochemical and biophysical properties. Altered RNA editing patterns have been observed in various neurological pathologies. Here, we present a comprehensive study of recoding by RNA editing in Alzheimer's disease (AD), the most common cause of irreversible dementia. We have used a targeted resequencing approach supplemented by a microfluidic-based high-throughput PCR coupled with next-generation sequencing to accurately quantify A-to-I RNA editing levels in a preselected set of target sites, mostly located within the coding sequence of synaptic genes. Overall, editing levels decreased in AD patients' brain tissues, mainly in the hippocampus and to a lesser degree in the temporal and frontal lobes. Differential RNA editing levels were observed in 35 target sites within 22 genes. These results may shed light on a possible association between the neurodegenerative processes typical for AD and deficient RNA editing.
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Affiliation(s)
- Khen Khermesh
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Michal Barak
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anita Annese
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy
| | - Chaim Wachtel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Eli Eisenberg
- Sagol School of Neuroscience and Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, 69978, Israel
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30
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De Leeneer K, Hellemans J, Steyaert W, Lefever S, Vereecke I, Debals E, Crombez B, Baetens M, Van Heetvelde M, Coppieters F, Vandesompele J, De Jaegher A, De Baere E, Coucke P, Claes K. Flexible, scalable, and efficient targeted resequencing on a benchtop sequencer for variant detection in clinical practice. Hum Mutat 2015; 36:379-87. [PMID: 25504618 DOI: 10.1002/humu.22739] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 08/07/2014] [Accepted: 12/02/2014] [Indexed: 12/30/2022]
Abstract
The release of benchtop next-generation sequencing (NGS) instruments has paved the way to implement the technology in clinical setting. The need for flexible, qualitative, and cost-efficient workflows is high. We used singleplex-PCR for highly efficient target enrichment, allowing us to reach the quality standards set in Sanger sequencing-based diagnostics. For the library preparation, a modified NexteraXT protocol was used, followed by sequencing on a MiSeq instrument. With an innovative pooling strategy, high flexibility, scalability, and cost-efficiency were obtained, independent of the availability of commercial kits. The approach was validated for ∼250 genes associated with monogenic disorders. An overall sensitivity (>99%) similar to Sanger sequencing was observed in combination with a positive predictive value of >98%. The distribution of coverage was highly uniform, guaranteeing a minimal number of gaps to be filled with alternative methods. ISO15189-accreditation was obtained for the workflow. A major asset of the singleplex PCR-based enrichment is that new targets can be easily implemented. Diagnostic laboratories have validated assays available ensuring that the proposed workflow can easily be adopted. Although our platform was optimized for constitutional variant detection of monogenic disease genes, it is now also used as a model for somatic mutation detection in acquired diseases.
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Affiliation(s)
- Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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31
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Hallast P, Batini C, Zadik D, Maisano Delser P, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Destro Bisol G, Dupuy BM, Eriksen HA, Jorde LB, King TE, Larmuseau MH, López de Munain A, López-Parra AM, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Geystelen A, Watkins S, Winney B, Jobling MA. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 2014; 32:661-73. [PMID: 25468874 PMCID: PMC4327154 DOI: 10.1093/molbev/msu327] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [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] [Indexed: 12/18/2022] Open
Abstract
Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eduardo Arroyo-Pardo
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Heidi A Eriksen
- Centre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland Utsjoki Health Care Centre, Utsjoki, Finland
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Turi E King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maarten H Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium Department of Imaging & Pathology, Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Ana M López-Parra
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | | | - Jelena Milasin
- School of Dental Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Horolma Pamjav
- Network of Forensic Science Institutes, Institute of Forensic Medicine, Budapest, Hungary
| | - Antti Sajantila
- Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - Matt Sears
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Scott Watkins
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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32
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Abstract
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
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Affiliation(s)
- Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Quentin Geissmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Julia Ferrari
- Department of Biology, University of York, York, United Kingdom
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554), CNRS, IRD, Université Montpellier 2, Montpellier, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom Sven Lovén Centre for Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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33
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Collopy LC, Walne AJ, Vulliamy TJ, Dokal IS. Targeted resequencing of 52 bone marrow failure genes in patients with aplastic anemia reveals an increased frequency of novel variants of unknown significance only in SLX4. Haematologica 2014; 99:e109-11. [PMID: 24763404 PMCID: PMC4077096 DOI: 10.3324/haematol.2014.105320] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Laura C Collopy
- Centre for Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London
| | - Amanda J Walne
- Centre for Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London
| | - Tom J Vulliamy
- Centre for Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London
| | - Inderjeet S Dokal
- Centre for Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London Barts Health NHS Trust, London, UK
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34
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Gui H, Bao JY, Tang CSM, So MT, Ngo DN, Tran AQ, Bui DH, Pham DH, Nguyen TL, Tong A, Lok S, Sham PC, Tam PKH, Cherny SS, Garcia-Barcelo MM. Targeted next-generation sequencing on Hirschsprung disease: a pilot study exploits DNA pooling. Ann Hum Genet 2014; 78:381-7. [PMID: 24947032 DOI: 10.1111/ahg.12076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 02/06/2014] [Accepted: 05/07/2014] [Indexed: 12/11/2022]
Abstract
To adopt an efficient approach of identifying rare variants possibly related to Hirschsprung disease (HSCR), a pilot study was set up to evaluate the performance of a newly designed protocol for next generation targeted resquencing. In total, 20 Chinese HSCR patients and 20 Chinese sex-matched individuals with no HSCR were included, for which coding sequences (CDS) of 62 genes known to be in signaling pathways relevant to enteric nervous system development were selected for capture and sequencing. Blood DNAs from eight pools of five cases or controls were enriched by PCR-based RainDance technology (RDT) and then sequenced on a 454 FLX platform. As technical validation, five patients from case Pool-3 were also independently enriched by RDT, indexed with barcode and sequenced with sufficient coverage. Assessment for CDS single nucleotide variants showed DNA pooling performed well (specificity/sensitivity at 98.4%/83.7%) at the common variant level; but relatively worse (specificity/sensitivity at 65.5%/61.3%) at the rare variant level. Further Sanger sequencing only validated five out of 12 rare damaging variants likely involved in HSCR. Hence more improvement at variant detection and sequencing technology is needed to realize the potential of DNA pooling for large-scale resequencing projects.
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Affiliation(s)
- Hongsheng Gui
- Department of Surgery, The University of Hong Kong, Hong Kong, SAR, China; Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
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Fernández-Marmiesse A, Morey M, Pineda M, Eiris J, Couce ML, Castro-Gago M, Fraga JM, Lacerda L, Gouveia S, Pérez-Poyato MS, Armstrong J, Castiñeiras D, Cocho JA. Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders. Orphanet J Rare Dis 2014; 9:59. [PMID: 24767253 PMCID: PMC4024120 DOI: 10.1186/1750-1172-9-59] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 10/16/2013] [Accepted: 04/07/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND With over 50 different disorders and a combined incidence of up to 1/3000 births, lysosomal storage diseases (LSDs) constitute a major public health problem and place an enormous burden on affected individuals and their families. Many factors make LSD diagnosis difficult, including phenotype and penetrance variability, shared signs and symptoms, and problems inherent to biochemical diagnosis. Developing a powerful diagnostic tool could mitigate the protracted diagnostic process for these families, lead to better outcomes for current and proposed therapies, and provide the basis for more appropriate genetic counseling. METHODS We have designed a targeted resequencing assay for the simultaneous testing of 57 lysosomal genes, using in-solution capture as the enrichment method and two different sequencing platforms. A total of 84 patients with high to moderate-or low suspicion index for LSD were enrolled in different centers in Spain and Portugal, including 18 positive controls. RESULTS We correctly diagnosed 18 positive blinded controls, provided genetic diagnosis to 25 potential LSD patients, and ended with 18 diagnostic odysseys. CONCLUSION We report the assessment of a next-generation-sequencing-based approach as an accessory tool in the diagnosis of LSDs, a group of disorders which have overlapping clinical profiles and genetic heterogeneity. We have also identified and quantified the strengths and limitations of next generation sequencing (NGS) technology applied to diagnosis.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | - Marcos Morey
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | - Merce Pineda
- Neuropediatra Fundación Hospital San Juan de Dios, CIBERER, Barcelona, Spain
| | - Jesús Eiris
- Servicio de Neuropediatría, Hospital Clínico Universitario de Santiago de Compostela, Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, Santiago de Compostela, La Coruña, Spain
| | - Maria Luz Couce
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | - Manuel Castro-Gago
- Servicio de Neuropediatría, Hospital Clínico Universitario de Santiago de Compostela, Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, Santiago de Compostela, La Coruña, Spain
| | - Jose Maria Fraga
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | - Lucia Lacerda
- Unidade de Bioquímica Genética, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar do Porto, Porto, Portugal
| | - Sofia Gouveia
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | | | - Judith Armstrong
- Servicio de Genética Molecular, Hospital San Juan de Dios, Barcelona, Spain
| | - Daisy Castiñeiras
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
| | - Jose A Cocho
- Unidad Diagnóstico y Tratamiento de Errores Congénitos del Metabolismo (Servicio de Neonatología), Facultad de Medicina y Odontología de la Universidad de Santiago de Compostela, 15706 Santiago de Compostela, La Coruña, Spain
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Trujillano D, Perez B, González J, Tornador C, Navarrete R, Escaramis G, Ossowski S, Armengol L, Cornejo V, Desviat LR, Ugarte M, Estivill X. Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing. Eur J Hum Genet 2014; 22:528-34. [PMID: 23942198 PMCID: PMC3953903 DOI: 10.1038/ejhg.2013.175] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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: 05/08/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 11/09/2022] Open
Abstract
Genetic diagnostics of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficient hyperphenylalaninemia (BH4DH) rely on methods that scan for known mutations or on laborious molecular tools that use Sanger sequencing. We have implemented a novel and much more efficient strategy based on high-throughput multiplex-targeted resequencing of four genes (PAH, GCH1, PTS, and QDPR) that, when affected by loss-of-function mutations, cause PKU and BH4DH. We have validated this approach in a cohort of 95 samples with the previously known PAH, GCH1, PTS, and QDPR mutations and one control sample. Pooled barcoded DNA libraries were enriched using a custom NimbleGen SeqCap EZ Choice array and sequenced using a HiSeq2000 sequencer. The combination of several robust bioinformatics tools allowed us to detect all known pathogenic mutations (point mutations, short insertions/deletions, and large genomic rearrangements) in the 95 samples, without detecting spurious calls in these genes in the control sample. We then used the same capture assay in a discovery cohort of 11 uncharacterized HPA patients using a MiSeq sequencer. In addition, we report the precise characterization of the breakpoints of four genomic rearrangements in PAH, including a novel deletion of 899 bp in intron 3. Our study is a proof-of-principle that high-throughput-targeted resequencing is ready to substitute classical molecular methods to perform differential genetic diagnosis of hyperphenylalaninemias, allowing the establishment of specifically tailored treatments a few days after birth.
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Affiliation(s)
- Daniel Trujillano
- Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Belén Perez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular UAM-CSIC, CIBERER, IDIPaz, Madrid, Spain
| | - Justo González
- Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Cristian Tornador
- Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular UAM-CSIC, CIBERER, IDIPaz, Madrid, Spain
| | - Georgia Escaramis
- Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Stephan Ossowski
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Lluís Armengol
- qGENOMICS, Quantitative Genomic Medicine Laboratories SL, Barcelona, Spain
| | - Verónica Cornejo
- Laboratorio de Genética y Enfermedades Metabólicas, INTA, Universidad de Chile, Santiago de Chile, Chile
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular UAM-CSIC, CIBERER, IDIPaz, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biologia Molecular UAM-CSIC, CIBERER, IDIPaz, Madrid, Spain
| | - Xavier Estivill
- Genomics and Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
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Geetha TS, Michealraj KA, Kabra M, Kaur G, Juyal RC, Thelma BK. Targeted deep resequencing identifies MID2 mutation for X-linked intellectual disability with varied disease severity in a large kindred from India. Hum Mutat 2014; 35:41-4. [PMID: 24115387 DOI: 10.1002/humu.22453] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 01/10/2013] [Accepted: 09/19/2013] [Indexed: 11/11/2022]
Abstract
We report a novel missense mutation (c.1040G>A, p.Arg347Gln) in MID2, which encodes ubiquitin ligase E3, as the likely cause of X-linked mental retardation in a large kindred. The mutation was observed in all affected and obligate carriers but not in any unaffected males of the family or in population controls (n = 200). When transiently expressed in HEK293T cell line, the mutation was found to abolish the function of the COS domain in the protein. The GFP-tagged mutant protein accumulated in the cytoplasm instead of binding to the cytoskeleton resulting in its altered subcellular localization. Screening of coding exons of this gene in additional 480 unrelated individuals with idiopathic intellectual disability identified another novel variation p.Asn343Ser. This study highlights the growing role of the ubiquitin pathway in intellectual disability and also, the difference in MID2 determined phenotype observed in this study compared with that of its paralogue MID1 reported in literature.
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Affiliation(s)
- Thenral S Geetha
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KFX, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J 2013; 76:494-505. [PMID: 23889683 PMCID: PMC4241023 DOI: 10.1111/tpj.12294] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/19/2013] [Indexed: 05/18/2023]
Abstract
Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Todd A Richmond
- Roche NimbleGen, Inc.500 South Rosa Road, Madison, WI, 53719, USA
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Leah Clissold
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Dharanya Sampath
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Sarah Ayling
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- † Present address:The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthias Pfeifer
- MIPS/IBIS, Helmholtz Zentrum MünchenD-85764, Neuherberg, Germany
| | - Mark D'Ascenzo
- Roche NimbleGen, Inc.500 South Rosa Road, Madison, WI, 53719, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State UniversityManhattan, KS, 66506, USA
| | - Pete E Hedley
- The James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
| | - Ana M Gonzales
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Klaus FX Mayer
- MIPS/IBIS, Helmholtz Zentrum MünchenD-85764, Neuherberg, Germany
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Robbie Waugh
- The James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mail )
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Swartz MD, Peng B, Reyes-Gibby C, Shete S. Using Ascertainment for Targeted Resequencing to Increase Power to Identify Causal Variants. Stat Interface 2011; 4:285-294. [PMID: 22468169 PMCID: PMC3316326 DOI: 10.4310/sii.2011.v4.n3.a3] [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] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Researchers continue to use genome-wide association studies (GWAS) to find the genetic markers associated with disease. Recent studies have added to the typical two-stage analysis a third stage that uses targeted resequencing on a randomly selected subset of the cases to detect the causal single-nucleotide polymorphism (SNP). We propose a design for targeted resequencing that increases the power to detect the causal variant. The design features an ascertainment scheme wherein only those cases with the presence of a risk allele are selected for targeted resequencing. We simulated a disease with a single causal SNP to evaluate our method versus a targeted resequencing design using randomly selected individuals. The simulation studies showed that ascertaining individuals for the targeted resequencing can substantially increase the power to detect a causal SNP, without increasing the false-positive rate.
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Affiliation(s)
- M. D. Swartz
- Division of Biostatistics, The University of Texas Health Science Center at Houston (UT Health), School of Public Health, Houston, TX 77030
| | - B. Peng
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - C. Reyes-Gibby
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - S. Shete
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
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