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Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping.
BMC Med Genet. 2016 Jan 04; 17:1.BM

Abstract

BACKGROUND

The widespread adoption of high-throughput sequencing technologies by genetic diagnostic laboratories has enabled significant expansion of their testing portfolios. Rare autosomal recessive conditions have been a particular focus of many new services. Here we report a cohort of 26 patients referred for genetic analysis of Joubert (JBTS) and Meckel-Gruber (MKS) syndromes, two clinically and genetically heterogeneous neurodevelopmental conditions that define a phenotypic spectrum, with MKS at the severe end.

METHODS

Exome sequencing was performed for all cases, using Agilent SureSelect v5 reagents and Illumina paired-end sequencing. For two cases medium-coverage (9×) whole genome sequencing was subsequently undertaken.

RESULTS

Using a standard analysis pipeline for the detection of single nucleotide and small insertion or deletion variants, molecular diagnoses were confirmed in 12 cases (4%). Seeking to determine whether our cohort harboured pathogenic copy number variants (CNV), in JBTS- or MKS-associated genes, targeted comparative read-depth analysis was performed using FishingCNV. These analyses identified a putative intragenic AHI1 deletion that included three exons spanning at least 3.4 kb and an intergenic MPP4 to TMEM237 deletion that included exons spanning at least 21.5 kb. Whole genome sequencing enabled confirmation of the deletion-containing alleles and precise characterisation of the mutation breakpoints at nucleotide resolution. These data were validated following development of PCR-based assays that could be subsequently used for "cascade" screening and/or prenatal diagnosis.

CONCLUSIONS

Our investigations expand the AHI1 and TMEM237 mutation spectrum and highlight the importance of performing CNV screening of disease-associated genes. We demonstrate a robust increasingly cost-effective CNV detection workflow that is applicable to all MKS/JBTS referrals.

Authors+Show Affiliations

Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. c.m.watson@leeds.ac.uk. School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. c.m.watson@leeds.ac.uk.Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. l.a.crinnion@leeds.ac.uk. School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. l.a.crinnion@leeds.ac.uk.Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. ianberry@nhs.net.School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. s.harrison@leeds.ac.uk.School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. c.lascelles@leeds.ac.uk.School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. umaan@leeds.ac.uk.Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. ruth.charlton1@nhs.net.Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. angus.dobbie@nhs.net.School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. i.m.carr@leeds.ac.uk.Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. d.t.bonthron@leeds.ac.uk. School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK. d.t.bonthron@leeds.ac.uk.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

26729329

Citation

Watson, Christopher M., et al. "Enhanced Diagnostic Yield in Meckel-Gruber and Joubert Syndrome Through Exome Sequencing Supplemented With Split-read Mapping." BMC Medical Genetics, vol. 17, 2016, p. 1.
Watson CM, Crinnion LA, Berry IR, et al. Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. BMC Med Genet. 2016;17:1.
Watson, C. M., Crinnion, L. A., Berry, I. R., Harrison, S. M., Lascelles, C., Antanaviciute, A., Charlton, R. S., Dobbie, A., Carr, I. M., & Bonthron, D. T. (2016). Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. BMC Medical Genetics, 17, 1. https://doi.org/10.1186/s12881-015-0265-z
Watson CM, et al. Enhanced Diagnostic Yield in Meckel-Gruber and Joubert Syndrome Through Exome Sequencing Supplemented With Split-read Mapping. BMC Med Genet. 2016 Jan 4;17:1. PubMed PMID: 26729329.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. AU - Watson,Christopher M, AU - Crinnion,Laura A, AU - Berry,Ian R, AU - Harrison,Sally M, AU - Lascelles,Carolina, AU - Antanaviciute,Agne, AU - Charlton,Ruth S, AU - Dobbie,Angus, AU - Carr,Ian M, AU - Bonthron,David T, Y1 - 2016/01/04/ PY - 2015/09/16/received PY - 2015/12/16/accepted PY - 2016/1/6/entrez PY - 2016/1/6/pubmed PY - 2016/5/12/medline SP - 1 EP - 1 JF - BMC medical genetics JO - BMC Med. Genet. VL - 17 N2 - BACKGROUND: The widespread adoption of high-throughput sequencing technologies by genetic diagnostic laboratories has enabled significant expansion of their testing portfolios. Rare autosomal recessive conditions have been a particular focus of many new services. Here we report a cohort of 26 patients referred for genetic analysis of Joubert (JBTS) and Meckel-Gruber (MKS) syndromes, two clinically and genetically heterogeneous neurodevelopmental conditions that define a phenotypic spectrum, with MKS at the severe end. METHODS: Exome sequencing was performed for all cases, using Agilent SureSelect v5 reagents and Illumina paired-end sequencing. For two cases medium-coverage (9×) whole genome sequencing was subsequently undertaken. RESULTS: Using a standard analysis pipeline for the detection of single nucleotide and small insertion or deletion variants, molecular diagnoses were confirmed in 12 cases (4%). Seeking to determine whether our cohort harboured pathogenic copy number variants (CNV), in JBTS- or MKS-associated genes, targeted comparative read-depth analysis was performed using FishingCNV. These analyses identified a putative intragenic AHI1 deletion that included three exons spanning at least 3.4 kb and an intergenic MPP4 to TMEM237 deletion that included exons spanning at least 21.5 kb. Whole genome sequencing enabled confirmation of the deletion-containing alleles and precise characterisation of the mutation breakpoints at nucleotide resolution. These data were validated following development of PCR-based assays that could be subsequently used for "cascade" screening and/or prenatal diagnosis. CONCLUSIONS: Our investigations expand the AHI1 and TMEM237 mutation spectrum and highlight the importance of performing CNV screening of disease-associated genes. We demonstrate a robust increasingly cost-effective CNV detection workflow that is applicable to all MKS/JBTS referrals. SN - 1471-2350 UR - https://www.unboundmedicine.com/medline/citation/26729329/Enhanced_diagnostic_yield_in_Meckel_Gruber_and_Joubert_syndrome_through_exome_sequencing_supplemented_with_split_read_mapping_ L2 - https://bmcmedgenet.biomedcentral.com/articles/10.1186/s12881-015-0265-z DB - PRIME DP - Unbound Medicine ER -