scholarly journals Rare Variant, Gene-Based Association Study of Hereditary Melanoma Using Whole-Exome Sequencing

2017 ◽  
Vol 109 (12) ◽  
Author(s):  
Mykyta Artomov ◽  
Alexander J Stratigos ◽  
Ivana Kim ◽  
Raj Kumar ◽  
Martin Lauss ◽  
...  
Keyword(s):  
Association Study ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Whole Exome ◽  
Variant Gene

scholarly journals Whole exome sequencing identifies genes associated with non-obstructive azoospermia

2020 ◽  
Author(s):  
Hongguo Zhang ◽  
Hui Huang ◽  
Xinyue Zhang ◽  
Wei Li ◽  
Yuting Jiang ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Biological Study ◽  
Obstructive Azoospermia ◽  
Novel Genes ◽  
Rare Variant Association ◽  
Whole Exome

AbstractBackgroundGenetic etiology is the main cause of non-obstructive azoospermia, but little is known about the landscape of the disease causative genes.ObjectiveTo identify the association of non-obstructive azoospermia and the putative causative genetic factors.Design, setting, and participantsA single-center perspective case-control study of 133 patients, with clinicopathologic non-obstructive azoospermia and 495 fertile men control was performed. Eleven trio families were available and enrolled from the 133 patients’ families.Outcome measurements and statistical analysisWhole exome sequencing based rare variant association study between the cases and controls was performed by means of gene burden association testing. Linkage analysis on the trio family was also described to screen the causative genes.Results and limitationsTotally 80 genes (p < 0.05) were identified associated with non-obstructive azoospermia (2 of which were previously reported), meanwhile 5 novel genes out of which were also found potentially causative through the linkage analysis on the trio families. The pathway enrichment analysis was also provided to assess the potential interaction between genes identified in this study and previously reported together. The 5 novel identified overlap genes by both above mentioned test with the rare mutations account for an overall 20% (26 /133 patients) incidence, together with the 2 known genes together would account for an overall 20% incidence for non-obstructive azoospermia in this study. The study is limited by the lack of functional biological study.ConclusionsFive novel genes were identified associated with non-obstructive azoospermia by means of both rare variant association study and linkage analysis through trio families. They could account for about 20% clinical incidence among the patients in our study.Patient summary133 infertile patients (11 of them with parents enrolled) with idiopathic non-obstructive azoospermia and 300 fertile male controls were recruited from single clinic center.All patients underwent semen analyses at least on three different occasions.

scholarly journals High-Frequency Exon Deletion of DNA Cross-Link Repair 1C Accounting for Severe Combined Immunodeficiency May Be Missed by Whole-Exome Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Feifan Xiao ◽  
Yulan Lu ◽  
Bingbing Wu ◽  
Bo Liu ◽  
Gang Li ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Severe Combined Immunodeficiency ◽  
Cell Receptor ◽  
Homozygous Deletion ◽  
Combined Immunodeficiency ◽  
Cross Link ◽  
Single Nucleotide Variants ◽  
Whole Exome

Next-generation sequencing (NGS) has been used to detect severe combined immunodeficiency (SCID) in patients, and some patients with DNA cross-link repair 1C (DCLRE1C) variants have been identified. Moreover, some compound variants, such as copy number variants (CNV) and single nucleotide variants (SNV), have been reported. The purpose of this study was to expand the genetic data related to patients with SCID carrying the compound DCLRE1C variant. Whole-exome sequencing (WES) was performed for genetic analysis, and variants were verified by performing Sanger sequencing or quantitative PCR. Moreover, we searched PubMed and summarized the data of the reported variants. Four SCID patients with DCLRE1C variants were identified in this study. WES revealed a homozygous deletion in the DCLRE1C gene from exons 1–5 in patient 1, exons 1–3 deletion and a novel rare variant (c.92T&gt;C, p.L31P) in patient 2, exons 1–3 deletion and a novel rare variant (c.328C&gt;G, p.L110V) in patient 3, and exons 1–4 deletion and a novel frameshift variant (c.449dup, p.His151Alafs*20) in patient 4. Based on literature review, exons 1–3 was recognized as a hotspot region for deletion variation. Moreover, we found that compound variations (CNV + SNV) accounted for approximately 7% variations in all variants. When patients are screened for T-cell receptor excision circles (TRECs), NGS can be used to expand genetic testing. Deletion of the DCLRE1C gene should not be ignored when a variant has been found in patients with SCID.

scholarly journals Whole-exome sequencing and gene-based rare variant association tests suggest that PLA2G4E might be a risk gene for panic disorder

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Yoshiro Morimoto ◽  
Mihoko Shimada-Sugimoto ◽  
Takeshi Otowa ◽  
Shintaro Yoshida ◽  
Akira Kinoshita ◽  
...  
Keyword(s):  
Panic Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Rare Variant Association ◽  
Association Tests ◽  
Risk Gene ◽  
Whole Exome

scholarly journals Nucleotide polymorphism in ARDS outcome: a whole exome sequencing association study

2021 ◽  
Vol 9 (9) ◽  
pp. 780-780
Author(s):  
Jing-Yuan Xu ◽  
Ai-Ran Liu ◽  
Zong-Sheng Wu ◽  
Jian-Feng Xie ◽  
Xiao-Xiao Qu ◽  
...  
Keyword(s):  
Association Study ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Nucleotide Polymorphism ◽  
Whole Exome

scholarly journals Whole exome sequencing identifies a rare variant in DAAM2 as a potential candidate in idiopathic pulmonary ossification

2019 ◽  
Vol 7 (14) ◽  
pp. 327-327
Author(s):  
Sheng-Wen Sun ◽  
Mei Zhou ◽  
Long Chen ◽  
Jiang-Hua Wu ◽  
Zhao-Ji Meng ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Potential Candidate ◽  
Whole Exome

scholarly journals Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Noha A. Yousri ◽  
Khalid A. Fakhro ◽  
Amal Robay ◽  
Juan L. Rodriguez-Flores ◽  
Robert P. Mohney ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Middle Eastern ◽  
Eastern Population ◽  
Whole Exome ◽  
Middle Eastern Population

scholarly journals Meta-analysis of whole-exome sequencing data from two independent cohorts finds no evidence for rare variant enrichment in Parkinson disease associated loci

PLoS ONE ◽  
2020 ◽  
Vol 15 (10) ◽  
pp. e0239824
Author(s):  
Johannes Jernqvist Gaare ◽  
Gonzalo Nido ◽  
Christian Dölle ◽  
Paweł Sztromwasser ◽  
Guido Alves ◽  
...  
Keyword(s):  
Parkinson Disease ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Meta Analysis ◽  
Sequencing Data ◽  
Exome Sequencing Data ◽  
Whole Exome ◽  
Whole Exome Sequencing Data

scholarly journals Whole-exome sequencing identifies a novel IHH insertion in an Ontario family with brachydactyly type A1

2018 ◽  
Vol 6 ◽  
pp. 2050313X1881871 ◽  
Author(s):  
Rosettia Ho ◽  
Adam D McIntyre ◽  
Brooke A Kennedy ◽  
Robert A Hegele
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variant ◽  
Autosomal Dominant ◽  
Dominant Mode ◽  
Indian Hedgehog ◽  
Whole Exome ◽  
Novel Variant ◽  
Exon 1 ◽  
Mode Of Inheritance

Isolated brachydactyly is an umbrella term describing disproportionally shortened fingers and toes, often following an autosomal dominant mode of inheritance. Various forms of brachydactyly have been characterized and several causative genes have been found, but many types remain genetically undefined. We describe an Ontario family with mild brachydactyly in which whole-exome sequencing identified a novel variant for brachydactyly type A1 (exon 1, c.285_287dupGAA, p.Glu95_Asn96insLys) in the Indian hedgehog ( IHH) gene. This rare variant co-segregated with affected status in the pedigree and was associated with (1) shortened middle phalange length by 21.1% ( p < 0.001); (2) shortened palm length by 13.8% ( p < 0.01); (3) reduced digit-palm ratio by 6.8% ( p < 0.03); and (4) reduced stature by 9.5% ( p < 0.001). We report the first IHH in-frame insertion causing brachydactyly type A1.

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