A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data

Demidov, German; Simakova, Tamara; Vnuchkova, Julia; Bragin, Anton

doi:10.1186/s12859-016-1272-6

Cited by 6 publications

(7 citation statements)

References 24 publications

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“…WES was used to indicate the general presence of the CNV, which was validated by touchdown PCR and Sanger sequencing. A more detailed description of the methods used can be found in the BMC Bioinformatics paper by Demidov et al ( 17 ). With the ongoing advances in sequencing technology and improvement in alignment techniques for large-scale data analysis, we were able to confirm that IL25 does not lie within the previously identified amplified region on chromosome 14, but rather 4 Mb downstream.…”

Section: Methodsmentioning

confidence: 99%

Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case

et al. 2018

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BackgroundWe investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood.AimTo identify causative functional genetic variants related to an undiagnosed primary immunodeficiency.MethodWhole genome microarray copy number variant (CNV) analysis was performed on the proband followed by whole exome sequencing (WES) and trio analysis of the proband and family members. A >4 kbp deletion identified by repeated CNV analysis of exome sequencing data along with three damaging missense single nucleotide variants were validated by Sanger sequencing in all family members. Confirmation of the causative role of the candidate gene was performed by qPCR and Western Blot analyses on the proband, family members and a healthy control.ResultsCNV identified our previously reported interleukin 25 amplification in the proband; however, the variant was not validated to be a candidate gene for immunodeficiency. WES trio analysis, data filtering and in silico prediction identified a novel, damaging (SIFT: 0; Polyphen 1; Grantham score: 101) and disease-causing (MutationTaster) single base mutation in the X chromosome (c.511C > T p.Arg171Trp) MSN gene not identified in the UCSC Genome Browser database. The mutation was validated by Sanger sequencing, confirming the proband was hemizygous X-linked recessive (–/T) at this locus and inherited the affected T allele from his non-symptomatic carrier mother (C/T), with other family members (father, sister) confirmed to be wild type (C/C). Western Blot analysis demonstrated an absence of moesin protein in lymphocytes derived from the proband, compared with normal expression in lymphocytes derived from the healthy control, father and mother. qPCR identified significantly lower MSN mRNA transcript expression in the proband compared to an age- and sex-matched healthy control subject in whole blood (p = 0.02), and lymphocytes (p = 0.01). These results confirmed moesin deficiency in the proband, directly causative of his immunodeficient phenotype.ConclusionThese findings confirm X-linked moesin-associated immunodeficiency in a proband previously undiagnosed up to 24 years of age. This study also highlights the utility of WES for the diagnosis of rare or novel forms of primary immunodeficiency disease.

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Section: Methodsmentioning

confidence: 99%

Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case

et al. 2018

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“…The resulting data was then processed using Illumina's VariantStudio software. CNV analysis was performed using Parseq Lab's CONVector tool for exon‐scale CNV detection 10 . When combined, these two analyses covered all variants included in the panel.…”

Section: Methodsmentioning

confidence: 99%

Pathogenic variant‐based preconception carrier screening in the Israeli Jewish population

et al. 2022

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Preconception carrier screening allows identification of couples at risk to have offspring with autosomal recessive and X‐linked disorders. In a current multiethnic world, screening based on self‐reported ancestry has limitations. Here we describe the findings of a comprehensive pan‐ethnic variant‐based carrier screening, using the Israeli Jewish population as a model. The cohort included 1696 individuals (848 couples) tested with the ‘MyScreen’ multigene panel. The panel covers 1206 variants spanning 385 genes, known in different Jewish ethnicities and local Arab, Druze and Bedouin populations. Out of these, 205 variants in 143 genes are Jewish founder variants. We identified 859 (50.6%), carriers of at least one variant in 151 genes. Importantly, 569 (66.2%) of carriers could be missed by the current Israeli screening program. In total, 1:40 (2.5%) of carrier couples were identified by the ‘MyScreen’ panel, compared with 1:144 (0.7%) found by the ethnicity‐based screening. Surprisingly, 90 individuals (10.5%) were carriers of variants “unexpected” for their reported origin, and 16 variants were previously unreported in Jewish patients. Our results support the advantages of variant‐based comprehensive carrier screening for detection of carriers and at‐risk couples in a diverse population with many founder disease‐causing variants.

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“…MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations [52]. More than two sets and up to ten sets of PCR primers are selected for Multiplexing to amplify those regions of the gene that are susceptible to deletion in DMD/BMD.…”

Section: Use Of Multiplex Pcr For Detection Of Dmdmentioning

confidence: 99%

Application of Multiplex PCR for Detection of Duchunne Muscular Dystrophy: A Childhood Neuromuscular Disorder

Srivastava¹,

Srivastava²

2018

J Neurol Neurosci

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Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder that affects 1 in 3,600 -6,000 males and is caused by mutation in the dystrophin gene. This is neuromuscular disorder with progressive muscle weakness, which predominantly affect males. Till date no absolute cure of the disease is available in clinical practice. Early diagnosis and timely management are requisite for DMD and it enhances the quality of life of patients. Various diagnostic approaches are available but due to accuracy, early detection and non-invasive method molecular tools are most remarkable in recent era. Multiplex PCR has emerged as one of the most convenient tools for screening of DMD in terms of its sensitivity, specificity, accuracy, cost effectiveness and time consumption. The current study emphasizes advantages and shortcomings of multiplex PCR with reference to most of the past studies along with its challenges for DMD detection in detail. Mutation detection is evidently crucial for diagnosis, as well as it may also be significant for future therapeutic purposes. Further research is important to elucidate specific mutation pattern in association with management and therapies of proband.

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A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data

Cited by 6 publications

References 24 publications

Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case

Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case

Pathogenic variant‐based preconception carrier screening in the Israeli Jewish population

Application of Multiplex PCR for Detection of Duchunne Muscular Dystrophy: A Childhood Neuromuscular Disorder

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