1
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Colbert BM, Lanting C, Smeal M, Blanton S, Dykxhoorn DM, Tang PC, Getchell RL, Velde H, Fehrmann M, Thorpe R, Chapagain P, Elkhaligy H, Kremer H, Yntema H, Haer-Wigman L, Redfield S, Sun T, Bruijn S, Plomp A, Goderie T, van de Kamp J, Free RH, Wassink-Ruiter JK, Widdershoven J, Vanhoutte E, Rotteveel L, Kriek M, van Dooren M, Hoefsloot L, de Gier HHW, Schaefer A, Kolbe D, Azaiez H, Rabie G, Aburayyan A, Kawas M, Kanaan M, Holder J, Usami SI, Chen Z, Dai P, Holt J, Nelson R, Choi BY, Shearer E, Smith RJH, Pennings R, Liu XZ. The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. Hum Genet 2024:10.1007/s00439-024-02648-3. [PMID: 38691166 DOI: 10.1007/s00439-024-02648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/21/2024] [Indexed: 05/03/2024]
Abstract
TMPRSS3-related hearing loss presents challenges in correlating genotypic variants with clinical phenotypes due to the small sample sizes of previous studies. We conducted a cross-sectional genomics study coupled with retrospective clinical phenotype analysis on 127 individuals. These individuals were from 16 academic medical centers across 6 countries. Key findings revealed 47 unique TMPRSS3 variants with significant differences in hearing thresholds between those with missense variants versus those with loss-of-function genotypes. The hearing loss progression rate for the DFNB8 subtype was 0.3 dB/year. Post-cochlear implantation, an average word recognition score of 76% was observed. Of the 51 individuals with two missense variants, 10 had DFNB10 with profound hearing loss. These 10 all had at least one of 4 TMPRSS3 variants predicted by computational modeling to be damaging to TMPRSS3 structure and function. To our knowledge, this is the largest study of TMPRSS3 genotype-phenotype correlations. We find significant differences in hearing thresholds, hearing loss progression, and age of presentation, by TMPRSS3 genotype and protein domain affected. Most individuals with TMPRSS3 variants perform well on speech recognition tests after cochlear implant, however increased age at implant is associated with worse outcomes. These findings provide insight for genetic counseling and the on-going design of novel therapeutic approaches.
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Affiliation(s)
- Brett M Colbert
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Cris Lanting
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Molly Smeal
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Derek M Dykxhoorn
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Pei-Ciao Tang
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
| | - Richard L Getchell
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Hedwig Velde
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirthe Fehrmann
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ryan Thorpe
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Heidy Elkhaligy
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger Yntema
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Tieqi Sun
- Boston Children's Hospital, Boston, USA
| | - Saskia Bruijn
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Astrid Plomp
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Thadé Goderie
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | - Rolien H Free
- Groningen University Medical Center, Groningen, The Netherlands
| | | | | | - Els Vanhoutte
- Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | | | | | | | - Amanda Schaefer
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Diana Kolbe
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Hela Azaiez
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Grace Rabie
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | | | - Mariana Kawas
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | - Moien Kanaan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | | | | | - Zhengyi Chen
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, USA
| | - Pu Dai
- PLA General Hospital, Beijing, China
| | | | - Rick Nelson
- Department of Otolaryngology, Indiana University School of Medicine, Indianapolis, USA
| | - Byung Yoon Choi
- Seoul National University Bundang Hospital, Seongnam, South Korea
| | | | | | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA.
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2
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Steyaert W, Haer-Wigman L, Pfundt R, Hellebrekers D, Steehouwer M, Hampstead J, de Boer E, Stegmann A, Yntema H, Kamsteeg EJ, Brunner H, Hoischen A, Gilissen C. Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation. Nat Commun 2023; 14:6845. [PMID: 37891200 PMCID: PMC10611741 DOI: 10.1038/s41467-023-42531-9] [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: 11/22/2022] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.
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Affiliation(s)
- Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Debby Hellebrekers
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Elke de Boer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Alexander Stegmann
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Han Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
- Radboud University Medical Center, Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands.
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3
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Khazeeva G, Sablauskas K, van der Sanden B, Steyaert W, Kwint M, Rots D, Hinne M, van Gerven M, Yntema H, Vissers L, Gilissen C. DeNovoCNN: a deep learning approach to de novo variant calling in next generation sequencing data. Nucleic Acids Res 2022; 50:e97. [PMID: 35713566 PMCID: PMC9508836 DOI: 10.1093/nar/gkac511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/19/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major challenge due to sequence errors, uneven coverage, and mapping artifacts. Here, we developed a deep convolutional neural network (CNN) DNM caller (DeNovoCNN), that encodes the alignment of sequence reads for a trio as 160\documentclass[12pt]{minimal}
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}{}$ \times$\end{document}164 resolution images. DeNovoCNN was trained on DNMs of 5616 whole exome sequencing (WES) trios achieving total 96.74% recall and 96.55% precision on the test dataset. We find that DeNovoCNN has increased recall/sensitivity and precision compared to existing DNM calling approaches (GATK, DeNovoGear, DeepTrio, Samtools) based on the Genome in a Bottle reference dataset and independent WES and WGS trios. Validations of DNMs based on Sanger and PacBio HiFi sequencing confirm that DeNovoCNN outperforms existing methods. Most importantly, our results suggest that DeNovoCNN is likely robust against different exome sequencing and analyses approaches, thereby allowing the application on other datasets. DeNovoCNN is freely available as a Docker container and can be run on existing alignment (BAM/CRAM) and variant calling (VCF) files from WES and WGS without a need for variant recalling.
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Affiliation(s)
- Gelana Khazeeva
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Karolis Sablauskas
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Bart van der Sanden
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Dmitrijs Rots
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Max Hinne
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands
| | - Marcel van Gerven
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands
| | - Helger Yntema
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Lisenka Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
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4
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Sallevelt SCEH, Stegmann APA, de Koning B, Velter C, Steyls A, van Esch M, Lakeman P, Yntema H, Esteki MZ, de Die-Smulders CEM, Gilissen C, van den Wijngaard A, Brunner HG, Paulussen ADC. Diagnostic exome-based preconception carrier testing in consanguineous couples: results from the first 100 couples in clinical practice. Genet Med 2021; 23:1125-1136. [PMID: 33742171 PMCID: PMC8187149 DOI: 10.1038/s41436-021-01116-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 01/20/2023] Open
Abstract
Purpose Consanguineous couples are at increased risk of being heterozygous for the same autosomal recessive (AR) disorder(s), with a 25% risk of affected offspring as a consequence. Until recently, comprehensive preconception carrier testing (PCT) for AR disorders was unavailable in routine diagnostics. Here we developed and implemented such a test in routine clinical care. Methods We performed exome sequencing (ES) for 100 consanguineous couples. For each couple, rare variants that could give rise to biallelic variants in offspring were selected. These variants were subsequently filtered against a gene panel consisting of ~2,000 genes associated with known AR disorders (OMIM-based). Remaining variants were classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, after which only likely pathogenic and pathogenic (class IV/V) variants, present in both partners, were reported. Results In 28 of 100 tested consanguineous couples (28%), likely pathogenic and pathogenic variants not previously known in the couple or their family were reported conferring 25% risk of affected offspring. Conclusion ES-based PCT provides a powerful diagnostic tool to identify AR disease carrier status in consanguineous couples. Outcomes provided significant reproductive choices for a higher proportion of these couples than previous tests.
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Affiliation(s)
- Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Melanie van Esch
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christine E M de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.,Donders center for Neuroscience, Radboudumc, Nijmegen, The Netherlands.,MHENS school of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands. .,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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5
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Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SMM, Adan IBJF, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJL, Shendure J, Nelen MR, Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem 2016; 63:503-512. [PMID: 27974384 DOI: 10.1373/clinchem.2016.263897] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Bart van Lier
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Alwin Rikken
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Tychon
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stijn M M Bertens
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Ivo B J F Adan
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bastiaan B Tops
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tomasz Stokowy
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hildegunn Høberg-Vetti
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Evan Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marcel R Nelen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands;
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
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6
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Mutmainah I, Nillesen W, Mundhofir F, Winarni T, Van der Burgt I, Yntema H, Faradz S. Clinical and molecular analysis of Noonan syndrome in Indonesia: a case report. PI 2016. [DOI: 10.14238/pi56.1.2016.62-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Noonan syndrome (NS; OMIM#163950) is a relatively common autosomal dominant disorder with a worldwide prevalence of approximately 1:1,000 to 1:2,500. The syndrome is characterized by distinctive facial features, congenital heart defects (CHD), and short stature. Distinctive facial features consist of a broad and high forehead, hypertelorism, downslanting palpebral fissures, a high arched palate, low set and posteriorly rotated ears with a thick helix, and a short neck with excess nuchal skin and low posterior hairline. Additional relatively frequent features include chest deformities, cryptorchidism in males, mild intellectual disability, and bleeding diathesis.1,2In 2001, missense mutations in
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7
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Matthijs G, Souche E, Alders M, Corveleyn A, Eck S, Feenstra I, Race V, Sistermans E, Sturm M, Weiss M, Yntema H, Bakker E, Scheffer H, Bauer P. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet 2015; 24:2-5. [PMID: 26508566 PMCID: PMC4795226 DOI: 10.1038/ejhg.2015.226] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/03/2015] [Accepted: 08/25/2015] [Indexed: 11/16/2022] Open
Abstract
We present, on behalf of EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of next-generation sequencing (NGS) applications for the diagnosis of genetic disorders. The work was performed by a group of laboratory geneticists and bioinformaticians, and discussed with clinical geneticists, industry and patients' representatives, and other stakeholders in the field of human genetics. The statements that were written during the elaboration of the guidelines are presented here. The background document and full guidelines are available as supplementary material. They include many examples to assist the laboratories in the implementation of NGS and accreditation of this service. The work and ideas presented by others in guidelines that have emerged elsewhere in the course of the past few years were also considered and are acknowledged in the full text. Interestingly, a few new insights that have not been cited before have emerged during the preparation of the guidelines. The most important new feature is the presentation of a ‘rating system' for NGS-based diagnostic tests. The guidelines and statements have been applauded by the genetic diagnostic community, and thus seem to be valuable for the harmonization and quality assurance of NGS diagnostics in Europe.
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Affiliation(s)
- Gert Matthijs
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Erika Souche
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Mariëlle Alders
- Department of Clinical Genetics, Academic Medical Centre (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anniek Corveleyn
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Sebastian Eck
- Center for Human Genetics and Laboratory Medicine, Martinsried, Germany
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valérie Race
- Center for Human Genetics, KU Leuven, Gasthuisberg, Laboratory for Molecular Diagnosis, Leuven, Belgium
| | - Erik Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Marc Sturm
- University Hospital of Tübingen, Institute of Medical Genetics and Applied Genomics, Tübingen, Germany
| | - Marjan Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Egbert Bakker
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Bauer
- University Hospital of Tübingen, Institute of Medical Genetics and Applied Genomics, Tübingen, Germany
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Moog U, Bierhals T, Brand K, Bautsch J, Biskup S, Brune T, Denecke J, de Die-Smulders CE, Evers C, Hempel M, Henneke M, Yntema H, Menten B, Pietz J, Pfundt R, Schmidtke J, Steinemann D, Stumpel CT, Van Maldergem L, Kutsche K. Phenotypic and molecular insights into CASK-related disorders in males. Orphanet J Rare Dis 2015; 10:44. [PMID: 25886057 PMCID: PMC4449965 DOI: 10.1186/s13023-015-0256-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/20/2015] [Indexed: 12/05/2022] Open
Abstract
Background Heterozygous loss-of-function mutations in the X-linked CASK gene cause progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH) and severe intellectual disability (ID) in females. Different CASK mutations have also been reported in males. The associated phenotypes range from nonsyndromic ID to Ohtahara syndrome with cerebellar hypoplasia. However, the phenotypic spectrum in males has not been systematically evaluated to date. Methods We identified a CASK alteration in 8 novel unrelated male patients by targeted Sanger sequencing, copy number analysis (MLPA and/or FISH) and array CGH. CASK transcripts were investigated by RT-PCR followed by sequencing. Immunoblotting was used to detect CASK protein in patient-derived cells. The clinical phenotype and natural history of the 8 patients and 28 CASK-mutation positive males reported previously were reviewed and correlated with available molecular data. Results CASK alterations include one nonsense mutation, one 5-bp deletion, one mutation of the start codon, and five partial gene deletions and duplications; seven were de novo, including three somatic mosaicisms, and one was familial. In three subjects, specific mRNA junction fragments indicated in tandem duplication of CASK exons disrupting the integrity of the gene. The 5-bp deletion resulted in multiple aberrant CASK mRNAs. In fibroblasts from patients with a CASK loss-of-function mutation, no CASK protein could be detected. Individuals who are mosaic for a severe CASK mutation or carry a hypomorphic mutation still showed detectable amount of protein. Conclusions Based on eight novel patients and all CASK-mutation positive males reported previously three phenotypic groups can be distinguished that represent a clinical continuum: (i) MICPCH with severe epileptic encephalopathy caused by hemizygous loss-of-function mutations, (ii) MICPCH associated with inactivating alterations in the mosaic state or a partly penetrant mutation, and (iii) syndromic/nonsyndromic mild to severe ID with or without nystagmus caused by CASK missense and splice mutations that leave the CASK protein intact but likely alter its function or reduce the amount of normal protein. Our findings facilitate focused testing of the CASK gene and interpreting sequence variants identified by next-generation sequencing in cases with a phenotype resembling either of the three groups. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Kristina Brand
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Jan Bautsch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | | | - Thomas Brune
- Universitätskinderklinik, Universitätsklinikum Magdeburg, Magdeburg, Germany.
| | - Jonas Denecke
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Neuropädiatrie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| | - Christine E de Die-Smulders
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht UMC+, Maastricht, The Netherlands.
| | - Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Marco Henneke
- Klinik für Kinder- und Jugendmedizin, Universitätsmedizin Göttingen, Göttingen, Germany.
| | - Helger Yntema
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
| | - Joachim Pietz
- Section of Neuropediatrics, Center for Child and Adolescent Medicine, Heidelberg, Germany.
| | - Rolph Pfundt
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Jörg Schmidtke
- Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover, Germany.
| | - Doris Steinemann
- Institut für Zell- und Molekularpathologie, Medizinische Hochschule Hannover, Hannover, Germany.
| | - Constance T Stumpel
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht UMC+, Maastricht, The Netherlands.
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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Kuechler A, Willemsen MH, Albrecht B, Bacino CA, Bartholomew DW, van Bokhoven H, van den Boogaard MJH, Bramswig N, Büttner C, Cremer K, Czeschik JC, Engels H, van Gassen K, Graf E, van Haelst M, He W, Hogue JS, Kempers M, Koolen D, Monroe G, de Munnik S, Pastore M, Reis A, Reuter MS, Tegay DH, Veltman J, Visser G, van Hasselt P, Smeets EEJ, Vissers L, Wieland T, Wissink W, Yntema H, Zink AM, Strom TM, Lüdecke HJ, Kleefstra T, Wieczorek D. De novo mutations in beta-catenin (CTNNB1) appear to be a frequent cause of intellectual disability: expanding the mutational and clinical spectrum. Hum Genet 2014; 134:97-109. [PMID: 25326669 DOI: 10.1007/s00439-014-1498-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
Recently, de novo heterozygous loss-of-function mutations in beta-catenin (CTNNB1) were described for the first time in four individuals with intellectual disability (ID), microcephaly, limited speech and (progressive) spasticity, and functional consequences of CTNNB1 deficiency were characterized in a mouse model. Beta-catenin is a key downstream component of the canonical Wnt signaling pathway. Somatic gain-of-function mutations have already been found in various tumor types, whereas germline loss-of-function mutations in animal models have been shown to influence neuronal development and maturation. We report on 16 additional individuals from 15 families in whom we newly identified de novo loss-of-function CTNNB1 mutations (six nonsense, five frameshift, one missense, two splice mutation, and one whole gene deletion). All patients have ID, motor delay and speech impairment (both mostly severe) and abnormal muscle tone (truncal hypotonia and distal hypertonia/spasticity). The craniofacial phenotype comprised microcephaly (typically -2 to -4 SD) in 12 of 16 and some overlapping facial features in all individuals (broad nasal tip, small alae nasi, long and/or flat philtrum, thin upper lip vermillion). With this detailed phenotypic characterization of 16 additional individuals, we expand and further establish the clinical and mutational spectrum of inactivating CTNNB1 mutations and thereby clinically delineate this new CTNNB1 haploinsufficiency syndrome.
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Affiliation(s)
- Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany,
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Iurian SI, Brunner H, Yntema H, Mehedintu B. Leopard Syndrome. Familial cases. Ro J Pediatr 2014. [DOI: 10.37897/rjp.2014.1.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
LEOPARD syndrome is a complex disorder characterized by multiple dysmorphogenetic features. Both syndromes LEOPARD and Noonan are caused by different mutations in the same gene (PTPN11). Authors emphasize diagnosis peculiarities in two related cases with facial dysmorphism. Index case is represented by a 10 year-old boy admitted for evaluation because of cephalofacial dysmorphism associated with mental disabilities. Family history: non-consanguineous parents; the father’s case and his sister with face dysmorphism. Clinical exam: short stature, impaired nutritional status, axillary freckles, widespread café-au-lait spots, face dysmorphism, webbed neck, skeletal anomalies and mental retardation. Blood investigations and cardiac ultrasonography: no anomalies. Differential diagnosis includes Noonan syndrome, Greig syndrome, type 1 neurofibromatosis, Albright syndrome. Regarding patient genetic evaluation: normal karyotype; DNA sequencing revealed mutation in PTPN11 gene suggestive for LEOPARD syndrome. Authors also found same mutation for probant’s father. Conclusions. Authors described two cases with dysmorphic skull, skeletal anomalies, skin pigmentation, mental disabilities and short stature, justifying further genetic evaluation that revealed a very rare disorder.
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Iurian SI, Brunner H, Yntema H, Mehedinţu B. Sindromul Leopard. Cazuri familiale. Ro J Pediatr 2014. [DOI: 10.37897/rjp.2014.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sindromul LEOPARD este o afecţiune ce include multiple anomalii dismorfogenetice. Sindromul LEOPARD, ca şi sindromul Noonan, este determinat de mutaţii ale genei PTPN11. Autorii menţionează particularităţile diagnostice la 2 cazuri înrudite cu dismorfism facial. Cazul index este reprezentat de băiat de 10 ani evaluat pentru dismorfism cranio-facial asociat cu retard mental. Antecedente heredo-colaterale: fără consangvinitate; tatăl pacientului şi soră cu dismorfism facial. Examenul clinic: retard staturo-ponderal, pistrui axilari, pete café-au-lait diseminate, dismorfism facial, pterigium coli, anomalii scheletice, retard mental. Investigaţiile sangvine şi eco-cardiografia: fără modificări. Pentru diagnosticul diferenţial s-au considerat sindroamele Noonan, Greig, neurofibromatoza tip 1, sindromul Mc Cune-Albright. Evaluarea genetică: cariotip normal; secvenţierea genei PTPN11 a relevat mutaţia ce confirmă sindromul LEOPARD. Analiza genetică a relevat aceeaşi mutaţie la tatăl pacientului. Concluzii. Autorii au descris 2 cazuri familiale cu craniu dismorf, anomalii scheletice, pigmentaţia pielii, dizabilităţi mentale şi statură mică, justificând evaluarea genetică care a identificat o afecţiune genetică foarte rară.
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Verhoeven WM, Egger JI, Koolen DA, Yntema H, Olgiati S, Breedveld GJ, Bonifati V, van de Warrenburg BP. Beta-propeller protein-associated neurodegeneration (BPAN), a rare form of NBIA: Novel mutations and neuropsychiatric phenotype in three adult patients. Parkinsonism Relat Disord 2014; 20:332-6. [DOI: 10.1016/j.parkreldis.2013.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/21/2013] [Accepted: 11/30/2013] [Indexed: 01/08/2023]
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Kaiser FJ, Ansari M, Braunholz D, Concepción Gil-Rodríguez M, Decroos C, Wilde JJ, Fincher CT, Kaur M, Bando M, Amor DJ, Atwal PS, Bahlo M, Bowman CM, Bradley JJ, Brunner HG, Clark D, Del Campo M, Di Donato N, Diakumis P, Dubbs H, Dyment DA, Eckhold J, Ernst S, Ferreira JC, Francey LJ, Gehlken U, Guillén-Navarro E, Gyftodimou Y, Hall BD, Hennekam R, Hudgins L, Hullings M, Hunter JM, Yntema H, Innes AM, Kline AD, Krumina Z, Lee H, Leppig K, Lynch SA, Mallozzi MB, Mannini L, McKee S, Mehta SG, Micule I, Mohammed S, Moran E, Mortier GR, Moser JAS, Noon SE, Nozaki N, Nunes L, Pappas JG, Penney LS, Pérez-Aytés A, Petersen MB, Puisac B, Revencu N, Roeder E, Saitta S, Scheuerle AE, Schindeler KL, Siu VM, Stark Z, Strom SP, Thiese H, Vater I, Willems P, Williamson K, Wilson LC, Hakonarson H, Quintero-Rivera F, Wierzba J, Musio A, Gillessen-Kaesbach G, Ramos FJ, Jackson LG, Shirahige K, Pié J, Christianson DW, Krantz ID, Fitzpatrick DR, Deardorff MA. Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance. Hum Mol Genet 2014; 23:2888-900. [PMID: 24403048 DOI: 10.1093/hmg/ddu002] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL, encoding a cohesin regulatory protein, account for >80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A, SMC3 and RAD21 genes, together account for ∼5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing. Most mutations identified are missense and de novo. Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS.
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Affiliation(s)
- Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Lübeck 23538, Germany
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van de Kamp JM, Betsalel OT, Mercimek-Mahmutoglu S, Abulhoul L, Grünewald S, Anselm I, Azzouz H, Bratkovic D, de Brouwer A, Hamel B, Kleefstra T, Yntema H, Campistol J, Vilaseca MA, Cheillan D, D’Hooghe M, Diogo L, Garcia P, Valongo C, Fonseca M, Frints S, Wilcken B, von der Haar S, Meijers-Heijboer HE, Hofstede F, Johnson D, Kant SG, Lion-Francois L, Pitelet G, Longo N, Maat-Kievit JA, Monteiro JP, Munnich A, Muntau AC, Nassogne MC, Osaka H, Ounap K, Pinard JM, Quijano-Roy S, Poggenburg I, Poplawski N, Abdul-Rahman O, Ribes A, Arias A, Yaplito-Lee J, Schulze A, Schwartz CE, Schwenger S, Soares G, Sznajer Y, Valayannopoulos V, Van Esch H, Waltz S, Wamelink MMC, Pouwels PJW, Errami A, van der Knaap MS, Jakobs C, Mancini GM, Salomons GS. Phenotype and genotype in 101 males with X-linked creatine transporter deficiency. J Med Genet 2013; 50:463-72. [DOI: 10.1136/jmedgenet-2013-101658] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Ropers HH, Hoeltzenbein M, Kalscheuer V, Yntema H, Hamel B, Fryns JP, Chelly J, Partington M, Gecz J, Moraine C. Nonsyndromic X-linked mental retardation: where are the missing mutations? Trends Genet 2003; 19:316-20. [PMID: 12801724 DOI: 10.1016/s0168-9525(03)00113-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Analysis of linkage intervals from 125 unrelated families with nonsyndromic X-linked mental retardation (NS-XLMR) has revealed that the respective gene defects are conspicuously clustered in defined regions of the human X-chromosome, with approximately 30% of all mutations being located on the proximal Xp. In 83% of these families, underlying gene defects are not yet known. Our observations should speed up the search for mutations that are still missing and pave the way for the molecular diagnosis of this common disorder.
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Affiliation(s)
- Hans-Hilger Ropers
- Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany.
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Kutsche K, Yntema H, Brandt A, Jantke I, Nothwang HG, Orth U, Boavida MG, David D, Chelly J, Fryns JP, Moraine C, Ropers HH, Hamel BC, van Bokhoven H, Gal A. Mutations in ARHGEF6, encoding a guanine nucleotide exchange factor for Rho GTPases, in patients with X-linked mental retardation. Nat Genet 2000; 26:247-50. [PMID: 11017088 DOI: 10.1038/80002] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
X-linked forms of mental retardation (XLMR) include a variety of different disorders and may account for up to 25% of all inherited cases of mental retardation. So far, seven X-chromosomal genes mutated in nonspecific mental retardation (MRX) have been identified: FMR2, GDI1, RPS6KA3, IL1RAPL, TM4SF2, OPHN1 and PAK3 (refs 2-9). The products of the latter two have been implicated in regulation of neural plasticity by controlling the activity of small GTPases of the Rho family. Here we report the identification of a new MRX gene, ARHGEF6 (also known as alphaPIX or Cool-2), encoding a protein with homology to guanine nucleotide exchange factors for Rho GTPases (Rho GEF). Molecular analysis of a reciprocal X/21 translocation in a male with mental retardation showed that this gene in Xq26 was disrupted by the rearrangement. Mutation screening of 119 patients with nonspecific mental retardation revealed a mutation in the first intron of ARHGEF6 (IVS1-11T-->C) in all affected males in a large Dutch family. The mutation resulted in preferential skipping of exon 2, predicting a protein lacking 28 amino acids. ARHGEF6 is the eighth MRX gene identified so far and the third such gene to encode a protein that interacts with Rho GTPases.
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Affiliation(s)
- K Kutsche
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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