Whole-exome sequencing of skin cancer: study is the most comprehensive view of melanoma’s genetic landscape

Prime ◽  
2011 ◽  
Vol 1 (2) ◽  
pp. 10-10
2019 ◽  
Vol 56 (6) ◽  
pp. 396-407 ◽  
Author(s):  
Kazuhiro Iwama ◽  
Takeshi Mizuguchi ◽  
Eri Takeshita ◽  
Eiji Nakagawa ◽  
Tetsuya Okazaki ◽  
...  

BackgroundRett syndrome (RTT) is a characteristic neurological disease presenting with regressive loss of neurodevelopmental milestones. Typical RTT is generally caused by abnormality of methyl-CpG binding protein 2 (MECP2). Our objective to investigate the genetic landscape of MECP2-negative typical/atypical RTT and RTT-like phenotypes using whole exome sequencing (WES).MethodsWe performed WES on 77 MECP2-negative patients either with typical RTT (n=11), atypical RTT (n=22) or RTT-like phenotypes (n=44) incompatible with the RTT criteria.ResultsPathogenic or likely pathogenic single-nucleotide variants in 28 known genes were found in 39 of 77 (50.6%) patients. WES-based CNV analysis revealed pathogenic deletions involving six known genes (including MECP2) in 8 of 77 (10.4%) patients. Overall, diagnostic yield was 47 of 77 (61.0 %). Furthermore, strong candidate variants were found in four novel genes: a de novo variant in each of ATPase H+ transporting V0 subunit A1 (ATP6V0A1), ubiquitin-specific peptidase 8 (USP8) and microtubule-associated serine/threonine kinase 3 (MAST3), as well as biallelic variants in nuclear receptor corepressor 2 (NCOR2).ConclusionsOur study provides a new landscape including additional genetic variants contributing to RTT-like phenotypes, highlighting the importance of comprehensive genetic analysis.


Author(s):  
Alain Calender ◽  
Yves Pacheco ◽  
Pierre Rollat Farnier ◽  
Claire Bardel ◽  
Pascal Seve ◽  
...  

Cells ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 118
Author(s):  
Caroline Cazin ◽  
Yasmine Neirijnck ◽  
Corinne Loeuillet ◽  
Lydia Wehrli ◽  
Françoise Kühne ◽  
...  

The genetic landscape of male infertility is highly complex. It is estimated that at least 4000 genes are involved in human spermatogenesis, but only few have so far been extensively studied. In this study, we investigated by whole exome sequencing two cases of idiopathic non-obstructive azoospermia (NOA) due to severe hypospermatogenesis. After variant filtering and prioritizing, we retained for each patient a homozygous loss-of-function (LoF) variant in a testis-specific gene, C1orf185 (c.250C>T; p.Gln84Ter) and CCT6B (c.615-2A>G), respectively. Both variants are rare according to the gnomAD database and absent from our local control cohort (n = 445). To verify the implication of these candidate genes in NOA, we used the CRISPR/Cas9 system to invalidate the mouse orthologs 4930522H14Rik and Cct6b and produced two knockout (KO) mouse lines. Sperm and testis parameters of homozygous KO adult male mice were analyzed and compared with those of wild-type animals. We showed that homozygous KO males were fertile and displayed normal sperm parameters and a functional spermatogenesis. Overall, these results demonstrate that not all genes highly and specifically expressed in the testes are essential for spermatogenesis, and in particular, we conclude that bi-allelic variants of C1orf185 and CCT6B are most likely not to be involved in NOA and male fertility.


2021 ◽  
Vol 1 (1) ◽  
pp. 1-16
Author(s):  
Marco Magistri ◽  
Lanie E. Happ ◽  
Jeremy Ramdial ◽  
XiaoQing Lu ◽  
Vasileios Stathias ◽  
...  

A comprehensive constellation of somatic nonsilent mutations and copy-number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors, we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NF-κB, NOTCH, and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets. Significance: We report systematic application of whole-exome sequencing and CN variations in OAMZL, revealing common alterations in regulation of NFAT signaling pathway that may facilitate identification of new therapies.


Author(s):  
Ryia-Illani Mohd Yunos ◽  
Nurul-Syakima Ab Mutalib ◽  
Sheau Sean Khor ◽  
Sazuita Saidin ◽  
Mohd Ridhwan Abd Razak ◽  
...  

Majority of colorectal cancer (CRC) patients are presented with advanced disease at diagnosis, particularly in cases of proximal CRCs. Little is known about the relationship between the genetic landscape and the anatomical location of the tumour; as well as the prognostication in CRC patients. The objectives of this study were to determine the somatic single nucleotide variants (SNV) and the cellular pathways between the proximal and distal CRCs. Whole exome sequencing was performed on the Ion Proton platform on 10 pairs of normal and CRC samples. The sequencing results were analysed using the Torrent Suite Software and the variants were annotated using ANNOVAR; followed by validation with Sanger sequencing. APC is the most frequently altered gene in both proximal and distal CRCs. KRAS and ATM genes were particularly altered in the proximal CRCs with a frequency of 60% and 40%, respectively. On the other hand, TP53 mutations did not show any CRC anatomical predominance. There were five recurrent novel variants in proximal CRCs and no recurrent variants identified in distal CRC. Wnt signalling pathway was the most frequently altered pathway in both proximal and distal CRCs whereas TGF-? and PI3K signalling pathways were predominantly altered in the proximal CRCs. We found that proximal CRCs presented with more variants and different altered pathways as compared to distal CRCs. However, further study in a larger series of samples coupled with functional studies will be required to confirm the identified variants and determine their roles in the pathogenesis of proximal and distal CRCs.


2021 ◽  
Vol 7 (2) ◽  
pp. e568
Author(s):  
Jose-Alberto Palma ◽  
Rachita Yadav ◽  
Dadi Gao ◽  
Lucy Norcliffe-Kaufmann ◽  
Susan Slaugenhaupt ◽  
...  

ObjectiveTo test the hypothesis that many patients presenting with congenital insensitivity to pain have lesser known or unidentified mutations not captured by conventional genetic panels, we performed whole-exome sequencing in a cohort of well-characterized patients with a clinical diagnosis of congenital hereditary sensory and autonomic neuropathy with unrevealing conventional genetic testing.MethodsWe performed whole-exome sequencing (WES) in 13 patients with congenital impaired or absent sensation to pain and temperature with no identified molecular diagnosis from a conventional genetic panel. Patients underwent a comprehensive phenotypic assessment including autonomic function testing, and neurologic and ophthalmologic examinations.ResultsWe identified known or likely pathogenic genetic causes of congenital insensitivity to pain in all 13 patients, spanning 9 genes, the vast majority of which were inherited in an autosomal recessive manner. These included known pathogenic variants (3 patients harboring mutations in TECPR2 and SCN11A), suspected pathogenic variants in genes described to cause congenital sensory and autonomic syndromes (7 patients harboring variants in NGF, LIFR, SCN9A, and PRDM12), and likely pathogenic variants in novel genes (4 patients harboring variants in SMPDL3A, PLEKHN1, and SCN10A).ConclusionsOur results expand the genetic landscape of congenital sensory and autonomic neuropathies. Further validation of some identified variants should confirm their pathogenicity. WES should be clinically considered to expedite diagnosis, reduce laboratory investigations, and guide enrollment in future gene therapy trials.


2014 ◽  
Vol 62 (S 02) ◽  
Author(s):  
M. Hitz ◽  
S. Al-Turki ◽  
A. Schalinski ◽  
U. Bauer ◽  
T. Pickardt ◽  
...  

2018 ◽  
Author(s):  
Yasemin Dincer ◽  
Michael Zech ◽  
Matias Wagner ◽  
Nikolai Jung ◽  
Volker Mall ◽  
...  

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