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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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Del Gobbo GF, Wang X, Couse M, Mackay L, Goldsmith C, Marshall AE, Liang Y, Lambert C, Zhang S, Dhillon H, Fanslow C, Rowell WJ, Marshall CR, Kernohan KD, Boycott KM. Long-read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development. Am J Med Genet A 2024; 194:e63522. [PMID: 38131126 DOI: 10.1002/ajmg.a.63522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease-associated variants and understand the genetic basis of many rare diseases. Long-read genome sequencing provides improved sequencing in highly repetitive, homologous, and low-complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short-read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi-generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE-VNTR-Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss-of-function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss-of-expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long-read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short-read genomic testing.
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Affiliation(s)
- Giulia F Del Gobbo
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Xueqi Wang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Madeline Couse
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Layla Mackay
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Claire Goldsmith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Aren E Marshall
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Yijing Liang
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Siyuan Zhang
- PacBio of California, Inc, Menlo Park, California, USA
| | | | | | | | | | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Newborn Screening Ontario, Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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3
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Pidaparti M, Geddes GC, Durbin MD. Clinical Genetic and Genomic Testing in Congenital Heart Disease and Cardiomyopathy. J Clin Med 2024; 13:2544. [PMID: 38731073 PMCID: PMC11084871 DOI: 10.3390/jcm13092544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Congenital heart disease (CHD) and cardiomyopathies are the leading cause of morbidity and mortality worldwide. These conditions are often caused by genetic factors, and recent research has shown that genetic and genomic testing can provide valuable information for patient care. By identifying genetic causes, healthcare providers can screen for other related health conditions, offer early interventions, estimate prognosis, select appropriate treatments, and assess the risk for family members. Genetic and genomic testing is now the standard of care in patients with CHD and cardiomyopathy. However, rapid advances in technology and greater availability of testing options have led to changes in recommendations for the most appropriate testing method. Several recent studies have investigated the utility of genetic testing in this changing landscape. This review summarizes the literature surrounding the clinical utility of genetic evaluation in patients with CHD and cardiomyopathy.
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Affiliation(s)
- Mahati Pidaparti
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Gabrielle C. Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Matthew D. Durbin
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Herman B Wells Center for Pediatric Research, 1044 W. Walnut, Indianapolis, IN 46202, USA
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Ten Berk de Boer E, Ameur A, Bunikis I, Ek M, Stattin EL, Feuk L, Eisfeldt J, Lindstrand A. Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation. Sci Rep 2024; 14:9000. [PMID: 38637641 PMCID: PMC11026446 DOI: 10.1038/s41598-024-59683-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/13/2024] [Indexed: 04/20/2024] Open
Abstract
Long-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of phased and non-phased de novo assemblies; (i) based on lrGS only and (ii) hybrid assemblies combining lrGS with optical mapping using lrGS reads with a median coverage of 34X. Variant calling detected both structural variants (SVs) and small variants and the accuracy of the small variant calling was compared with those called with short-read genome sequencing (srGS). The de novo and hybrid assemblies had high quality and contiguity with N50 of 62.85 Mb, enabling a near telomere to telomere assembly with less than a 100 contigs per haplotype. Notably, we successfully identified the centromeric breakpoint of the translocation. A concordance of 92% was observed when comparing small variant calling between srGS and lrGS. In summary, our findings underscore the remarkable potential of lrGS as a comprehensive and accurate solution for the analysis of SVs and small variants. Thus, lrGS could replace a large battery of genetic tests that were used for the diagnosis of a single symptomatic translocation carrier, highlighting the potential of lrGS in the realm of digital karyotyping.
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Affiliation(s)
- Esmee Ten Berk de Boer
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 65, Solna, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 36, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 36, Uppsala, Sweden
| | - Marlene Ek
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Eva-Lena Stattin
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 36, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 36, Uppsala, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden.
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76, Stockholm, Sweden.
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 65, Solna, Sweden.
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76, Stockholm, Sweden
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Li JX, Meng LR, Hou BK, Hao XL, Wang DJ, Qu LH, Li ZH, Zhang L, Jin X. Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing. Curr Med Sci 2024; 44:419-425. [PMID: 38619684 DOI: 10.1007/s11596-024-2865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/07/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVE Autosomal recessive bestrophinopathy (ARB), a retinal degenerative disease, is characterized by central visual loss, yellowish multifocal diffuse subretinal deposits, and a dramatic decrease in the light peak on electrooculogram. The potential pathogenic mechanism involves mutations in the BEST1 gene, which encodes Ca2+-activated Cl- channels in the retinal pigment epithelium (RPE), resulting in degeneration of RPE and photoreceptor. In this study, the complete clinical characteristics of two Chinese ARB families were summarized. METHODS Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing was performed on the probands to screen for disease-causing gene mutations, and Sanger sequencing was applied to validate variants in the patients and their family members. RESULTS Two novel mutations, c.202T>C (chr11:61722628, p.Y68H) and c.867+97G>A, in the BEST1 gene were identified in the two Chinese ARB families. The novel missense mutation BEST1 c.202T>C (p.Y68H) resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1. Another novel variant, BEST1 c.867+97G>A (chr11:61725867), located in intron 7, might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators. CONCLUSION Our findings represent the first use of third-generation sequencing (TGS) to identify novel BEST1 mutations in patients with ARB, indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes. The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.
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Affiliation(s)
- Jia-Xun Li
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Ling-Rui Meng
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Bao-Ke Hou
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Xiao-Lu Hao
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Da-Jiang Wang
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Ling-Hui Qu
- Department of Ophthalmology, the 74th Army Group Hospital, Guangzhou, 510318, China
| | - Zhao-Hui Li
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Lei Zhang
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Xin Jin
- Department of Senior Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, 100853, China.
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Hoshino A, Oana Y, Ohi Y, Maeda Y, Omori M, Takada Y, Ikeda T, Sotome K, Maeda H, Yanagisawa T, Takeuchi O, Kuronuma S, Sangai T, Shibahara Y, Murakumo Y, Saegusa M, Kanomata N, Nagasawa S, Yamaguchi R, Yoshida M, Kozuka Y, Matsumoto H, Tsugawa K, Maeda I. Using the DNA Integrity Number to Analyze DNA Quality in Specimens Collected from Liquid-Based Cytology after Fine-Needle Aspiration of Breast Tumors and Lesions. Acta Cytol 2024; 68:145-152. [PMID: 38555634 DOI: 10.1159/000538071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/25/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Cancer genome analysis using next-generation sequencing requires adequate and high-quality DNA samples. Genomic analyses were conventionally performed using formalin-fixed paraffin-embedded sections rather than cytology samples such as cell block or smear specimens. Specimens collected from liquid-based cytology (LBC) have the potential to be sources of high-quality DNA suitable for genetic analysis even after long-term storage. METHODS We collected breast tumor/lesion fractions from 92 residual LBC specimens using fine-needle aspiration (FNA) biopsy, including breast carcinoma (1 invasive carcinoma and 4 ductal carcinomas in situ), papillomatous lesion (5 intraductal papillomas), and fibroepithelial lesion (19 phyllodes tumors and 53 fibroadenomas) samples, and others (1 ductal adenoma, 1 hamartoma, 1 fibrocystic disease, and 7 unknown). DNA was extracted from all samples and subjected to DNA integrity number (DIN) score analysis. RESULTS Average DIN score collected from 92 LBC specimens was significantly higher score. In addition, high-quality DNA with high DIN values (7.39 ± 0.80) was successfully extracted more than 12 months after storage of residual LBC specimens. CONCLUSION Residual LBC specimens collected from FNA of the breast were verified to carry high-quality DNA and could serve as an alternate source for genetic analysis.
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Affiliation(s)
- Akiyoshi Hoshino
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan,
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan,
| | - Yoshiyasu Oana
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yasuyo Ohi
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Yukari Maeda
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Masako Omori
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Yuki Takada
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Tadashi Ikeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keiichi Sotome
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Hinako Maeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takako Yanagisawa
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takafumi Sangai
- Department of Surgery, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yukiko Shibahara
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yoshiki Murakumo
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Naoki Kanomata
- Department of Pathology, St. Lukes International Hospital, Tokyo, Japan
| | - Satoi Nagasawa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba, Japan
| | - Rin Yamaguchi
- Department of Pathology, Nagasaki University Hospital, Nagasaki City, Nagasaki, Japan
| | - Masayuki Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Kozuka
- Department of Pathology, Mie University Hospital, Tsu, Japan
| | | | - Koichiro Tsugawa
- Divison of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ichiro Maeda
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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8
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Farrow E, Jay A, Means J, Younger S, Biswell R, Koseva B, Thiffault I, Pastinen T, Pappas K, Toriello H. Case of CLPB deficiency solved by HiFi long read genome sequencing and RNAseq. Am J Med Genet A 2023; 191:2908-2912. [PMID: 37548286 DOI: 10.1002/ajmg.a.63365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/03/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Affiliation(s)
- Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - John Means
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Scott Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Rebecca Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Kara Pappas
- Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Helga Toriello
- College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
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9
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Yamamoto N, Balciuniene J, Hartman T, Diaz-Miranda MA, Bedoukian E, Devkota B, Lawrence A, Golenberg N, Patel M, Tare A, Chen R, Schindler E, Choi J, Kaur M, Charles S, Chen J, Fanning EA, Dechene E, Cao K, Jill MR, Rajagopalan R, Bayram Y, Dulik MC, Germiller J, Conlin LK, Krantz ID, Luo M. Comprehensive Gene Panel Testing for Hearing Loss in Children: Understanding Factors Influencing Diagnostic Yield. J Pediatr 2023; 262:113620. [PMID: 37473993 DOI: 10.1016/j.jpeds.2023.113620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/17/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
OBJECTIVE To evaluate factors influencing the diagnostic yield of comprehensive gene panel testing (CGPT) for hearing loss (HL) in children and to understand the characteristics of undiagnosed probands. STUDY DESIGN This was a retrospective cohort study of 474 probands with childhood-onset HL who underwent CGPT between 2016 and 2020 at a single center. Main outcomes and measures included the association between clinical variables and diagnostic yield and the genetic and clinical characteristics of undiagnosed probands. RESULTS The overall diagnostic yield was 44% (209/474) with causative variants involving 41 genes. While the diagnostic yield was high in the probands with congenital, bilateral, and severe HL, it was low in those with unilateral, noncongenital, or mild HL; cochlear nerve deficiency; preterm birth; neonatal intensive care unit admittance; certain ancestry; and developmental delay. Follow-up studies on 49 probands with initially inconclusive CGPT results changed the diagnostic status to likely positive or negative outcomes in 39 of them (80%). Reflex to exome sequencing on 128 undiagnosed probands by CGPT revealed diagnostic findings in 8 individuals, 5 of whom had developmental delays. The remaining 255 probands were undiagnosed, with 173 (173/255) having only a single variant in the gene(s) associated with autosomal recessive HL and 28% (48/173) having a matched phenotype. CONCLUSION CGPT efficiently identifies the genetic etiologies of HL in children. CGPT-undiagnosed probands may benefit from follow-up studies or expanded testing.
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Affiliation(s)
- Nobuko Yamamoto
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA; Division of Otolaryngology, Department of Surgical Specialties, National Center for Children's Health and Development, Tokyo, Japan; Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; PerkinElmer Genomics, Pittsburgh, PA
| | - Tiffiney Hartman
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maria Alejandra Diaz-Miranda
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Emma Bedoukian
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Batsal Devkota
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Audrey Lawrence
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Netta Golenberg
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maha Patel
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Archana Tare
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Robert Chen
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emma Schindler
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jiwon Choi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maninder Kaur
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah Charles
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jiani Chen
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth A Fanning
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Dechene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Murrell R Jill
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yavuz Bayram
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - John Germiller
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Otorhinolaryngology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ian D Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
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10
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Szalai C. Arguments for and against the whole-genome sequencing of newborns. Am J Transl Res 2023; 15:6255-6263. [PMID: 37969196 PMCID: PMC10641337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
Recent decades have brought enormous progress in both genetics and genomics, as well as in information technology (IT). The sequence of the human genome is now known, and although our knowledge is far from complete, great progress has been made in understanding how the genome works. With the developments in storage capacity, artificial intelligence, and learning algorithms, we are now able to learn and interpret complex systems such as the human genome in a very short time. Perhaps the most important goal of learning about the human genome is to understand diseases better: how they develop; how their processes can be prevented or slowed down; and after diseases have developed, how they can be cured or their symptoms alleviated. The vast majority of diseases have a genetic background, i.e., genes, sequence variations, and gene-gene interactions play a role in most diseases to a greater or lesser extent. Accordingly, the first step is to discover which genes, or genomic variants, cause or contribute to the development of a particular disease in a given patient. Given that an individual's genome remains virtually unchanged throughout their life (with one or two exceptions, such as in the case of cancer, which is caused by somatic mutations), it might be considered advantageous to sequence the genome of every person at birth. In this paper, we set out to show the possible benefits of sequencing the entire genome of every human being at birth, while also discussing the main arguments against it.
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Affiliation(s)
- Csaba Szalai
- Department of Genetics, Cell and Immunobiology, Semmelweis University1089 Budapest, Hungary
- Heim Pál Children’s Hospital1089 Budapest, Hungary
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11
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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12
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Hamvas A, Chaudhari BP, Nogee LM. Genetic testing for diffuse lung diseases in children. Pediatr Pulmonol 2023. [PMID: 37191361 DOI: 10.1002/ppul.26447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Newly developing genomic technologies are an increasingly important part of clinical care and thus, it is not only important to understand the technologies and their limitations, but to also interpret the findings in an actionable fashion. Clinical geneticists and genetic counselors are now an integral part of the clinical team and are able to bridge the complexities of this rapidly changing science between the bedside clinicians and patients. This manuscript reviews the terminology, the current technology, some of the known genetic disorders that result in lung disease, and indications for genetic testing with associated caveats. Because this field is evolving quickly, we also provide links to websites that provide continuously updated information important for integrating genomic technology results into clinical decision-making.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bimal P Chaudhari
- Divisions of Genetics and Genomic Medicine, Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lawrence M Nogee
- Department of Pediatrics, Eudowood Neonatal Pulmonary Division, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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