scholarly journals Whole Exome-Sequencing of Pooled Genomic DNA Samples to Detect Quantitative Trait Loci in Esotropia and Exotropia of Strabismus in Japanese

Life ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 41
Author(s):  
Jingjing Zhang ◽  
Toshihiko Matsuo ◽  
Ichiro Hamasaki ◽  
Kazuhiro Sato
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Quantitative Trait ◽  
Genomic Dna ◽  
Window Size ◽  
Japanese Patients ◽  
Normal Group ◽  
Exome Capture ◽  
Rank Test ◽  
Whole Exome

Background: Esotropia and exotropia are two major phenotypes of comitant strabismus. It remains controversial whether esotropia and exotropia would share common genetic backgrounds. In this study, we used a quantitative trait locus (QTL)-sequencing pipeline for diploid plants to screen for susceptibility loci of strabismus in whole exome sequencing of pooled genomic DNAs of individuals. Methods: Pooled genomic DNA (2.5 ng each) of 20 individuals in three groups, Japanese patients with esotropia and exotropia, and normal members in the families, was sequenced twice after exome capture, and the first and second sets of data in each group were combined to increase the read depth. The SNP index, as the ratio of variant genotype reads to all reads, and Δ(SNP index) values, as the difference of SNP index between two groups, were calculated by sliding window analysis with a 4 Mb window size and 10 kb slide size. The rows of 200 “N”s were inserted as a putative 200-b spacer between every adjoining locus to depict Δ(SNP index) plots on each chromosome. SNP positions with depth <20 as well as SNP positions with SNP index of <0.3 were excluded. Results: After the exclusion of SNPs, 12,242 SNPs in esotropia/normal group and 12,108 SNPs in exotropia/normal group remained. The patterns of the Δ(SNP index) plots on each chromosome appeared different between esotropia/normal group and exotropia/normal group. When the consecutive groups of SNPs on each chromosome were set at three patterns: SNPs in each cytogenetic band, 50 consecutive sliding SNPs, and SNPs in 4 Mb window size with 10 kb slide size, p values (Wilcoxon signed rank test) and Q values (false discovery rate) in a few loci as Manhattan plots showed significant differences in comparison between the Δ(SNP index) in the esotropia/normal group and exotropia/normal group. Conclusions: The pooled DNA sequencing and QTL mapping approach for plants could provide overview of genetic background on each chromosome and would suggest different genetic backgrounds for two major phenotypes of comitant strabismus, esotropia and exotropia.

scholarly journals A domestic cat whole exome sequencing resource for trait discovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alana R. Rodney ◽  
Reuben M. Buckley ◽  
Robert S. Fulton ◽  
Catrina Fronick ◽  
Todd Richmond ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Diseases ◽  
Domestic Cat ◽  
Whole Genome Sequence ◽  
Exome Capture ◽  
Single Nucleotide Variants ◽  
Whole Exome ◽  
Olfactory Receptor Genes ◽  
Feline Model

AbstractOver 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.

Diagnostic Efficacy of Whole-Exome Sequencing in 250 Patients with Congenital Bone Marrow Failure

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4385-4385
Author(s):  
Hideki Muramatsu ◽  
Yusuke Okuno ◽  
Kenichi Yoshida ◽  
Sayoko Doisaki ◽  
Asahito Hama ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Clinical Practice ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Sanger Sequencing ◽  
Bone Marrow Failure ◽  
Exome Capture ◽  
Diagnostic Efficacy ◽  
Hematopoietic Stem ◽  
Whole Exome

Abstract Introduction: Congenital bone marrow failure syndromes (CBMFSs) are a heterogeneous class of diseases with overlapping phenotypes. Therefore, a precise and comprehensive genetic diagnostic system is strongly warranted to arrive at appropriate clinical decisions to avoid ineffective therapies and/or lethal complications of allogeneic hematopoietic stem cell transplantation. However, a large panel of newly identified causative genes of CBMFSs have been identified in recent years; therefore, it is virtually impossible to establish a routine genetic diagnostic test using conventional Sanger sequencing. Whole-exome sequencing (WES) is a promising solution for the diagnosis of inherited diseases because it tests virtually all genes simultaneously. For the introduction of WES into clinical practice, it is necessary to clarify whether this technique has superior diagnostic efficacy to conventional clinical genetic tests. Methods: We performed WES in 250 patients with CBMFSs lacking genetic diagnoses. Exome capture was performed using the SureSelect® Human All Exon V3–5 kit (Agilent Technologies, Santa Clara, CA, USA), which covers all known coding exons, followed by massively parallel sequencing using the HiSeq 2000 Sequencing System (Illumina, San Diego, CA, USA). Our established pipeline for WES (genomon: http://genomon.hgc.jp/exome/) detected >20,000 candidate variants per patient. Diagnoses were based on variants of 130 genes with pathogenicities confirmed by published studies. Results: Genetic diagnoses were possible in 68 patients (27%). The best efficacy was achieved in patients with Fanconi anemia [35/73, 48%; FANCG (n = 17), FANCA (n = 14), FANCB (n = 1), FANCF (n = 1), SLX4 (n = 1), and BRCA2 (n = 1)], although Sanger sequencing was not applied because of the large sizes of its causative genes. Encouraging results were obtained in patients with Diamond–Blackfan anemia [11/ 61, 18%; RPS26 (n = 3), RPS7 (n = 2), RPS19 (n = 2), RPL5 (n = 2), RPL35A (n = 1), and RPL11 (n = 1)] and dyskeratosis congenita [7/29, 24%; TERT (n = 3), TINF2 (n = 2), and DKC1 (n = 2)]. Five genetic diagnoses (7%) were inconsistent with clinical diagnoses, possibly because of overlapping disease phenotypes. Conclusion: Relative to conventional genetic testing, WES was found to be effective for the diagnoses of CBMFSs. Furthermore, the efficacy of WES will increase as our knowledge of gene mutations expands. In conclusion, the use of WES in clinical practice is warranted. Disclosures No relevant conflicts of interest to declare.

Utility of Whole Exome Sequencing in Diagnosis of Pediatric Platelet Disorders: A Subanalysis of the Pediseq Study

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3726-3726
Author(s):  
Edward J Romasko ◽  
Sawona Biswas ◽  
Batsal Devkota ◽  
Jayaraman Vijayakumar ◽  
Sowmyra Jairam ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Positive Family History ◽  
Exome Capture ◽  
Functional Evaluation ◽  
Whole Exome ◽  
Platelet Disorder ◽  
Uncertain Significance ◽  
History Of ◽  
Platelet Disorders

Abstract Background: Inherited Platelet Disorders (IPD) are individually rare disorders that have many different molecular causes. Diagnosis of IPD is often complicated by the need for complex testing that is not readily available at many centers and the lack of available testing to define the molecular cause of some disorders. While some platelet disorders are sufficiently defined by functional characterization, recent data suggests that some platelet disorders may predispose to significant other complications including cancer predisposition, myelofibrosis or hearing loss. Therefore, it may be important to establish a molecular diagnosis to better counsel families about necessary follow up and possible risks. The goal of this study was to determine the diagnostic yield of whole exome sequencing in a cohort of 22 pediatric patients with clinical presentation suggesting an underlying genetic cause (or positive family history of platelet disorder with no prior genetic diagnosis). Methods: Peripheral blood was collected from patients identified as likely to have an inherited platelet disorder after informed consent. Samples were also obtained from parents and siblings for co-segregation and variant calling. Genomic DNA was extracted manually using the Gentra Puregene Blood Kit. Exome capture was performed using the Agilent SureSelect v4 and 100 base paired end sequencing was done on an IlluminaHiSeq 2000 with 100X average coverage. Sequencing reads were generated in FASTQ format and mapped to human genome GRCh37 (hg19) and Novoalign v2.08 was used for optimal alignment. Disease-related variants were extracted from HGMD to identify variants that might be missed. Variant filtering and pathogenicity classification was performed using a customized pipeline and manual curation. We identified 53 genes of interest and on average across all exomes with an indication for a platelet disorder, bases were sequenced at a minimum depth of 15X to be considered covered within an exon. 80.4% of exons were 100% covered with this technology completely, while 10.4% of exons were partially covered (>40 to <100% bases) and 9.2% of exons were not covered (<40% of bases covered at a minimum of 15X depth). Results: 22 patients were enrolled over a 12-month period. Overall, 82% of patients had variants identified in platelet related genes on whole exome sequencing with 64% of patients returning at least one variant of uncertain significance (14) and 23% (5) patients returning definite positive results. One patient referred for further work up carried the initial diagnosis of ITP, but had macrothrombocytopenia since early childhood and bleeding out of proportion to the platelet count. Flow cytometry and functional studies performed on referral suggested possible Bernard Soulier Syndrome and sequencing confirmed homozygous pathogenic mutation in GP9. One patient with congenital thrombocytopenia and history of intracranial hemorrhage with a similarly affected sibling had confirmed pathogenic MYH9 mutation, allowing clinicians to offer prenatal diagnosis during a third pregnancy. One patient with a significant bleeding phenotype was a compound heterozygote for two novel RASGRP2 variants, but the functional significance of those variants is uncertain and further studies are underway to determine whether these variants are causative. 18% of patients (4) had negative sequencing results (no reportable variants in platelet related genes identified). Conclusions: Whole exome sequencing can be a powerful diagnostic tool in identifying the molecular cause of disease in a cohort of patients with suspected inherited platelet disorders. The majority of patients, however, will receive results of uncertain significance and centers that undertake this testing will require an infrastructure to allow for further functional evaluation, which will help in reclassification of these variants, and ensure that results are correctly interpreted. Clinicians who undertake ES to diagnose IPD need to understand limitations of the test as well as the full significance of results that may be returned. Disclosures Lambert: Novartis: Consultancy.

scholarly journals Whole-Exome Sequencing in Myelodysplastic Syndromes with 5q Deletion

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4635-4635
Author(s):  
Vera Adema ◽  
Laura Palomo ◽  
María Díez-Campelo ◽  
Mar Mallo ◽  
Leonor Arenillas ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Board Of Directors ◽  
Whole Exome Sequencing ◽  
Myelodysplastic Syndromes ◽  
Genomic Dna ◽  
Research Funding ◽  
Sequencing Data ◽  
Advisory Committees ◽  
Whole Exome ◽  
Increased Risk

Abstract INTRODUCTION Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid stem cell disorders that are highly prevalent in elderly populations. MDS are characterized by inefficient hematopoiesis, peripheral blood (PB) cytopenias, and increased risk of transformation to acute myeloid leukemia (AML; 20–30% of patients with MDS). Around 50% of MDS patients carry at least one karyotypic aberration. The interstitial deletion of the long arm of chromosome 5 ([del(5q)] is the most common aberration, accounting for almost 30% of abnormal MDS karyotype. Various studies supports a favorable prognosis of MDS with isolated del(5q) with an excellent response to lenalidomide treatment. In order to describe the molecular events associated with MDS and del(5q) we performed whole-exome sequencing (WES)(assessing 334,378 exons) of tumor-normal paired samples from 20 MDS patients to unravel the genetic basis of MDS with del(5q). The analysis is ongoing and the complete results will be presented in the meeting. METHODS A total of 50 samples from 20 patients with MDS, with del(5q) were collected. For each diagnostic sample, we performed Conventional G-banding cytogenetics and fluorescence in situ hybridization (FISH, to confirm or dismiss del(5q)) and SNP arrays with Cytoscan HD (Affymetrix). These samples included: 20 tumor samples at diagnosis, 20 control samples and 10 samples after diagnosis, during lenalidomide treatment (5) or at the moment of relapse (5) in order to compare the genetic status before and during the treatment. Genomic DNA from tumor cells was obtained from bone marrow (BM) samples or from PB granulocytes. As a source of constitutional DNA we used CD3+T cells from each patient by isolating by magnetic-activated cell sorting. WES targeted capture was carried out on 7μg of genomic DNA, using the SureSelect Human Exome Kit 51Mb version 4.Libraries were sequenced on an Illumina HiSeq2000. Sequencing data will be analyzed using an in-house bioinformatics pipeline as previously reported. RESULTS Our preliminary analysis of these 20 new patients by WES confirmed our previous analyses with mutations in well described genes as ASXL1, JAK2 and TET2, but not in genes RUNX1, SF3B1 and SRSF2. In those patients we found two patients with missense mutation in TP53, one of the patients had an isolated del(5q) and is receiving lenalidomide treatment, and the other one had a complex karyotype. According to our prior analyses, in which 249 non-silent somatic variants were detected, we look forward to validate these mutations in this new series of patients. CONCLUSIONS We envision to validate these previous results with the new sequencing data of more patients with MDS and del(5q). We expect to measure somatic mutations that vary in abundance after lenalidomide treatment, potentially identifying mutations associated with resistance or relapse. ACKNOWLEDGEMENTS: This work has been supported (in part) by a grants from Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Spain (PI 11/02010); by Red Temática de Investigación Cooperativa en Cáncer (RTICC, FEDER) (RD07/0020/2004; RD12/0036/0044); 2014 SGR225 (GRE) Generalitat de Catalunya; Fundació Internacional Josep Carreras; Obra Social “la Caixa”; Sociedad Española de Hematología y Hemoterapia (SEHH)and Celgene Spain. FOOTNOTES Rafael Bejar and Francesc Sole contributed equally. Disclosures Díez-Campelo: Novartis, Celgene: Honoraria, Research Funding. Xicoy:Celgene: Honoraria. Cañizo:Celgene, Jansen-Cilag, Arry, Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. sanchez-Garcia:Celgene: Honoraria, Research Funding. Bejar:Celgene: Membership on an entity's Board of Directors or advisory committees; Genoptix Medical Laboratory: Consultancy, Honoraria, Licensed IP, no royalties Patents & Royalties, Membership on an entity's Board of Directors or advisory committees. Sole:Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding.

scholarly journals A domestic cat whole exome sequencing resource for trait discovery

2020 ◽  
Author(s):  
Alana R. Rodney ◽  
Reuben M. Buckley ◽  
Robert S. Fulton ◽  
Catrina Fronick ◽  
Todd Richmond ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Diseases ◽  
Sex Chromosome ◽  
Cost Effective ◽  
Domestic Cat ◽  
Whole Genome Sequence ◽  
Exome Capture ◽  
Variant Discovery ◽  
Whole Exome

AbstractOver 94 million domestic cats are considered pets, who, as our companions, are also susceptible to cancers, common and rare diseases. Whole exome sequencing (WES) is a cost-effective strategy to study their putative disease-causing variants. Presented is ~35.8 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. WES was conducted on 41 cats from various breeds with known and unknown diseases and traits, including 10 cats with prior whole genome sequence (WGS) data available, to test WES capture probe performance. A WES and WGS comparison was completed to understand variant discovery capability of each platform. At ~80x exome coverage, the percent of on-target base coverage >20x was 96.4% with an average of 10.4% off-target. For variant discovery, greater than 98% of WGS SNPs were also discovered by WES. Platform specific variants were mainly restricted to a small number of sex chromosome and olfactory receptor genes. Within the 41 cats with ~31 diseases and normal traits, 45 previously known disease or trait causal variants were observed, such as Persian progressive retinal degeneration and hydrocephalus. Novel candidate variants for polycystic kidney disease and atrichia in the Peterbald breed were also identified as well as a new cat patient with a known variant for cystinuria. These results show the discovery potential of deep exome sequencing to validate existing disease gene models and identify novel gene candidate alleles for many common and rare diseases in cats.

scholarly journals Wessim: a whole-exome sequencing simulator based on in silico exome capture

2013 ◽  
Vol 29 (8) ◽  
pp. 1076-1077 ◽  
Author(s):  
Sangwoo Kim ◽  
Kyowon Jeong ◽  
Vineet Bafna
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
In Silico ◽  
Exome Capture ◽  
Whole Exome

Integrated comprehensive high-throughput kinomics profiling and whole exome sequencing of penile squamous cell cancer (PSCC).

2014 ◽  
Vol 32 (4_suppl) ◽  
pp. 383-383
Author(s):  
Amitkumar N. Mehta ◽  
Christopher Willey ◽  
Michael Crowley ◽  
Joshua Anderson ◽  
Dongquan Chen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Squamous Cell ◽  
Normal Tissue ◽  
Squamous Cell Cancer ◽  
Cell Cancer ◽  
The Cancer Genome Atlas ◽  
Exome Capture ◽  
Matched Normal Tissue ◽  
Whole Exome

383 Background: Molecular drivers in penile squamous cell cancer (PSCC), an orphan malignancy, remain unclear. The Cancer Genome Atlas (TCGA) is not studying PSCC and the Catalogue of Somatic Mutations in Cancer (COSMIC) investigators have reported only targeted analyses of PSCC. We report the first integrated analyses of comprehensive kinomics and whole exome sequencing (seq) in tumors from patients (pts) with PSCC . Methods: We performed integrated functional kinomics profiling and comprehensive exome-seq of two frozen tissue samples from men with PSCC with a matched normal tissue procured from the Cooperative Human Tissue Network (CHTN). Kinomic profiling was performed using the PamStation 12 high-content phospho-peptide substrate microarray system (PamGene International). The protein tyrosine kinome and serine/threonine kinome PamChips were used to measure global kinase activity by detecting phosphorylation of various peptides through FITC-labeled antibodies. Upstream kinase prediction was performed using a scoring algorithm that incorporates the phosphonet database (www.phosphonet.ca). Exome capture was performed with the Agilent SureSelect v5 kit and whole exome-seq was done on the Illumina HiSeq2000 with paired end 100bp chemistry. Results: In the single patient, paired kinomics analysis comparing the tumor sample to adjacent normal tissue, the HER family (EGFR, ERBB2, 3 and 4), AXL, TYRO3 and SYK kinases were the most active. When combining the two tumors in an unpaired analysis against the normal sample, the HER (EGFR, ERBB2, 3 and 4), MER, FRK, and FAK, kinases showed increased activity. When comparing whole exome-seq of the two PSCC samples with normal, among the affected genes were CCDC181, ZNF717, MUC4, HGC6.3, NOTCH1, STK11, SIRPB1, SKA3, PDE6B, FAT1, CACNA2D1, USP17L11, MNT, and CEP89. We are evaluating 10 PSCC tumors and matched normal tissue by kinomics and whole exome-seq and will present these complete data and analysis at the conference. Conclusions: In our preliminary analysis of pts that underwent the first reported integrated kinomics and whole exome-seq performed in PSCC, we identified multiple potential therapeutic targets in tumors.

Identification of novel mutations in Emirati subjects with Autosomal Dominant Familial Hypercholesterolemia (ADFH) in the United Arab Emirates by whole exome sequencing (WES): The WORTH study (Whole exOme sequencing of emiRaTi FH subjects) (Preprint)

2021 ◽  
Author(s):  
Yajnavalka Banerjee ◽  
Wael Al Mahmeed ◽  
Noushad Karuvantevida ◽  
Syeda Kiran Shahzadi ◽  
Alawi Al-Sheikh Ali
Keyword(s):  
Exome Sequencing ◽  
Familial Hypercholesterolemia ◽  
Whole Exome Sequencing ◽  
United Arab Emirates ◽  
Genomic Dna ◽  
Autosomal Dominant ◽  
Screening Program ◽  
Receptor Gene ◽  
Elevated Serum ◽  
Whole Exome

BACKGROUND Familial hypercholesterolemia (FH) is an autosomal-dominant disorder and is characterized by elevated serum levels of low-density lipoprotein cholesterol (LDL-C) that could dramatically increase the risk of developing cardiovascular diseases (CVD). FH is predominantly associated with mutations in three major genes, LDL receptor gene (LDLR), the apolipoprotein B gene (APOB), and the proprotein convertase subtilisin/kexin 9 gene (PCSK9). OBJECTIVE The aim of the present work will be to identify novel FH-causing genetic variants in Emirati patients diagnosed with autosomal dominant FH, using Simon-Broome diagnostic criteria (SBDC). METHODS Genomic DNA will be isolated from 30 patients diagnosed as definite FH using SBDC on the basis of the presence of family history of tendon xanthomas. Genomic DNA will be sheared into 100-400 bp, subjected to Illumina paired-end DNA library preparation, enriched for target sequences and will be sequenced using the HiSeq 2000 platform (Illumina). RESULTS Blood samples from FH-diagnosed Emirati people have been collected. Genomic DNA from 22 people has successfully been isolated, amplified for targeted exons and sent for sequencing. CONCLUSIONS This study will prove to be the first step in building an effective cascade screening program for the diagnosis of FH, tailored for the Emirati, population.

Familial occurrence of brain arteriovenous malformation: a novel ACVRL1 mutation detected by whole exome sequencing

2016 ◽  
Vol 126 (6) ◽  
pp. 1879-1883 ◽  
Author(s):  
Baran Yılmaz ◽  
Zafer Orkun Toktaş ◽  
Akın Akakın ◽  
Semra Işık ◽  
Kaya Bilguvar ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Exome Capture ◽  
Heterozygous Mutation ◽  
Sequencing Analysis ◽  
Whole Exome ◽  
Brain Avm ◽  
Study Results ◽  
Turkish Family ◽  
Cranial Mri

OBJECTIVEBrain arteriovenous malformations (AVMs) can occur in patients with hereditary hemorrhagic telangiectasia (HHT). However, brain AVM without HHT has also been reported. Using whole exome sequencing, the authors performed comprehensive genomic characterization of a 6-person Turkish family with 3 cases of brain AVM without HHT.METHODSThree siblings with brain AVM, one of whom also had spinal AVM, were evaluated. The parents and the fourth sibling had no AVM on cranial MRI. The authors performed a whole exome capture and Illumina sequencing on blood samples from 2 siblings with AVM.RESULTSAn ACVRL1 heterozygous mutation (p.Lys332Glu) was identified in 2 patients via whole exome sequencing. Variant segregation was confirmed using direct Sanger sequencing.CONCLUSIONSStudy results suggested that whole exome sequencing analysis is particularly useful in cases of locus heterogeneity and uncertain diagnostic classification schemes in patients with hereditary brain AVM.

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