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Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny D, Fatih JM, Yesil G, Elçioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res 2024; 52:e18. [PMID: 38153174 PMCID: PMC10899794 DOI: 10.1093/nar/gkad1223] [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: 07/12/2023] [Revised: 11/18/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul 34093, Turkey
| | - Nursel H Elçioglu
- Department of Pediatric Genetics, Marmara University Medical Faculty, Istanbul and Eastern Mediterranean University Faculty of Medicine, Mersin 10, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, 34480 Istanbul, Turkey
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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3
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Hirschi OR, Felker SA, Rednam SP, Vallance KL, Parsons DW, Roy A, Cooper GM, Plon SE. Combined Bioinformatic and Splicing Analysis of Likely Benign Intronic and Synonymous Variants Reveals Evidence for Pathogenicity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.30.23297632. [PMID: 37961416 PMCID: PMC10635218 DOI: 10.1101/2023.10.30.23297632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Current clinical variant analysis pipelines focus on coding variants and intronic variants within 10-20 bases of an exon-intron boundary that may affect splicing. The impact of newer splicing prediction algorithms combined with in vitro splicing assays on rare variants currently considered Benign/Likely Benign (B/LB) is unknown. Methods Exome sequencing data from 576 pediatric cancer patients enrolled in the Texas KidsCanSeq study were filtered for intronic or synonymous variants absent from population databases, predicted to alter splicing via SpliceAI (>0.20), and scored as potentially deleterious by CADD (>10.0). Total cellular RNA was extracted from monocytes and RT-PCR products analyzed. Subsequently, rare synonymous or intronic B/LB variants in a subset of genes submitted to ClinVar were similarly evaluated. Variants predicted to lead to a frameshifted splicing product were functionally assessed using an in vitro splicing reporter assay in HEK-293T cells. Results KidsCanSeq exome data analysis revealed a rare, heterozygous, intronic variant (NM_177438.3(DICER1):c.574-26A>G) predicted by SpliceAI to result in gain of a secondary splice acceptor site. The proband had a personal and family history of pleuropulmonary blastoma consistent with DICER1 syndrome but negative clinical sequencing reports. Proband RNA analysis revealed alternative DICER1 transcripts including the SpliceAI-predicted transcript.Similar bioinformatic analysis of synonymous or intronic B/LB variants (n=31,715) in ClinVar from 61 Mendelian disease genes yielded 18 variants, none of which could be scored by MaxEntScan. Eight of these variants were assessed (DICER1 n=4, CDH1 n=2, PALB2 n=2) using in vitro splice reporter assay and demonstrated abnormal splice products (mean 66%; range 6% to 100%). Available phenotypic information from submitting laboratories demonstrated DICER1 phenotypes in 2 families (1 variant) and breast cancer phenotypes for PALB2 in 3 families (2 variants). Conclusions Our results demonstrate the power of newer predictive splicing algorithms to highlight rare variants previously considered B/LB in patients with features of hereditary conditions. Incorporation of SpliceAI annotation of existing variant data combined with either direct RNA analysis or in vitro assays has the potential to identify disease-associated variants in patients without a molecular diagnosis.
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Affiliation(s)
- Owen R Hirschi
- Baylor College of Medicine, Houston, Texas
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas
| | | | - Surya P Rednam
- Baylor College of Medicine, Houston, Texas
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas
| | | | - D Williams Parsons
- Baylor College of Medicine, Houston, Texas
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas
| | | | | | - Sharon E Plon
- Baylor College of Medicine, Houston, Texas
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas
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4
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Reurink J, Weisschuh N, Garanto A, Dockery A, van den Born LI, Fajardy I, Haer-Wigman L, Kohl S, Wissinger B, Farrar GJ, Ben-Yosef T, Pfiffner FK, Berger W, Weener ME, Dudakova L, Liskova P, Sharon D, Salameh M, Offenheim A, Heon E, Girotto G, Gasparini P, Morgan A, Bergen AA, ten Brink JB, Klaver CC, Tranebjærg L, Rendtorff ND, Vermeer S, Smits JJ, Pennings RJ, Aben M, Oostrik J, Astuti GD, Corominas Galbany J, Kroes HY, Phan M, van Zelst-Stams WA, Thiadens AA, Verheij JB, van Schooneveld MJ, de Bruijn SE, Li CH, Hoyng CB, Gilissen C, Vissers LE, Cremers FP, Kremer H, van Wijk E, Roosing S. Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction. HGG ADVANCES 2023; 4:100181. [PMID: 36785559 PMCID: PMC9918427 DOI: 10.1016/j.xhgg.2023.100181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A significant number of individuals with a rare disorder such as Usher syndrome (USH) and (non-)syndromic autosomal recessive retinitis pigmentosa (arRP) remain genetically unexplained. Therefore, we assessed subjects suspected of USH2A-associated disease and no or mono-allelic USH2A variants using whole genome sequencing (WGS) followed by an improved pipeline for variant interpretation to provide a conclusive diagnosis. One hundred subjects were screened using WGS to identify causative variants in USH2A or other USH/arRP-associated genes. In addition to the existing variant interpretation pipeline, a particular focus was put on assessing splice-affecting properties of variants, both in silico and in vitro. Also structural variants were extensively addressed. For variants resulting in pseudoexon inclusion, we designed and evaluated antisense oligonucleotides (AONs) using minigene splice assays and patient-derived photoreceptor precursor cells. Biallelic variants were identified in 49 of 100 subjects, including novel splice-affecting variants and structural variants, in USH2A or arRP/USH-associated genes. Thirteen variants were shown to affect USH2A pre-mRNA splicing, including four deep-intronic USH2A variants resulting in pseudoexon inclusion, which could be corrected upon AON treatment. We have shown that WGS, combined with a thorough variant interpretation pipeline focused on assessing pre-mRNA splicing defects and structural variants, is a powerful method to provide subjects with a rare genetic condition, a (likely) conclusive genetic diagnosis. This is essential for the development of future personalized treatments and for patients to be eligible for such treatments.
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Affiliation(s)
- Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pediatrics, Amalia’s Children Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Adrian Dockery
- The School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Isabelle Fajardy
- Centre de Biologie Pathologie Génétique, CHU de Lille, Lille, France
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - G. Jane Farrar
- The School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Tamar Ben-Yosef
- The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fatma Kivrak Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
- Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | | | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Manar Salameh
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ashley Offenheim
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elise Heon
- Departments of Ophthalmology and Vision Sciences, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
| | - Giorgia Girotto
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
| | - Caroline C.W. Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, The Kennedy Center, Copenhagen University Hospital, 2600 Glostrup, Denmark
- Institute of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nanna D. Rendtorff
- Department of Clinical Genetics, The Kennedy Center, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Sascha Vermeer
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jeroen J. Smits
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center of Utrecht, Utrecht, the Netherlands
| | - Ronald J.E. Pennings
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jaap Oostrik
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh D.N. Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | | | - Hester Y. Kroes
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center of Utrecht, Utrecht, the Netherlands
| | - Milan Phan
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Rijnstate Hospital, Arnhem, the Netherlands
| | | | | | - Joke B.G.M. Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Mary J. van Schooneveld
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, the Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Catherina H.Z. Li
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carel B. Hoyng
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P.M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erwin van Wijk
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Hearing & Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
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5
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Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf G, Boerwinkle E, Muzny DM, Gibbs R, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience 2022; 12:giac125. [PMID: 36644891 PMCID: PMC9841152 DOI: 10.1093/gigascience/giac125] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/24/2022] [Accepted: 12/08/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from the analysis of comparatively small and homogeneous sample sets. FINDINGS We have developed xAtlas, a single-sample variant caller for single-nucleotide variants (SNVs) and small insertions and deletions (indels) in NGS data. xAtlas features rapid runtimes, support for CRAM and gVCF file formats, and retraining capabilities. xAtlas reports SNVs with 99.11% recall and 98.43% precision across a reference HG002 sample at 60× whole-genome coverage in less than 2 CPU hours. Applying xAtlas to 3,202 samples at 30× whole-genome coverage from the 1000 Genomes Project achieves an average runtime of 1.7 hours per sample and a clear separation of the individual populations in principal component analysis across called SNVs. CONCLUSIONS xAtlas is a fast, lightweight, and accurate SNV and small indel calling method. Source code for xAtlas is available under a BSD 3-clause license at https://github.com/jfarek/xatlas.
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Affiliation(s)
- Jesse Farek
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Hughes
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Institute of Genomic Medicine, Columbia University, New York, NY 10027, USA
| | - William Salerno
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aishwarya Pisupati
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adam Mansfield
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Olga Krasheninina
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Adam C English
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
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