scholarly journals Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens

2012 ◽  
Vol 40 (14) ◽  
pp. e107-e107 ◽  
Author(s):  
Shawn E. Yost ◽  
Erin N. Smith ◽  
Richard B. Schwab ◽  
Lei Bao ◽  
HyunChul Jung ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genome Sequence ◽  
Somatic Mutations ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Confidence ◽  
Formalin Fixed

scholarly journals ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data

2018 ◽  
Author(s):  
Shuto Hayashi ◽  
Rui Yamaguchi ◽  
Shinichi Mizuno ◽  
Mitsuhiro Komura ◽  
Satoru Miyano ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Somatic Mutations ◽  
Sequence Data ◽  
Point Mutations ◽  
Human Leukocyte ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Germline Variants ◽  
Hla Genes ◽  
Hla Genotyping

AbstractAlthough human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. Furthermore, there is no method to identify the sequences of unknown HLA types not registered in HLA databases. We developed a Bayesian model, called ALPHLARD, that collects reads potentially generated from HLA genes and accurately determines a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 6-digit resolution. Furthermore, ALPHLARD can detect rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data. We illustrate the capability of ALPHLARD using 253 WES data and 25 WGS data from Illumina platforms. By comparing the results of HLA genotyping from SBT and amplicon sequencing methods, ALPHLARD achieved 98.8% for WES data and 98.5% for WGS data at 4-digit resolution. We also detected three somatic point mutations and one case of loss of heterozygosity in the HLA genes from the WGS data. ALPHLARD showed good performance for HLA genotyping even from low-coverage data. It also has a potential to detect rare germline variants and somatic mutations in HLA genes. It would help to fill in the current gaps in HLA reference databases and unveil the immunological significance of somatic mutations identified in HLA genes.

scholarly journals High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Adrien M. Butty ◽  
Tatiane C. S. Chud ◽  
Filippo Miglior ◽  
Flavio S. Schenkel ◽  
Arun Kommadath ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Genome Sequence ◽  
Copy Number ◽  
Copy Number Variants ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Confidence ◽  
Array Data ◽  
Genotype Array

scholarly journals Whole Genome Sequence Analysis Suggests Intratumoral Heterogeneity in Dissemination of Breast Cancer to Lymph Nodes

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e115346 ◽  
Author(s):  
Kevin Blighe ◽  
Laura Kenny ◽  
Naina Patel ◽  
David S. Guttery ◽  
Karen Page ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Sequence Analysis ◽  
Lymph Nodes ◽  
Genome Sequence ◽  
Intratumoral Heterogeneity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene

Whole-Genome Sequence Isolation, Chromosome Location, and Characteriza-tion of Primary Auxin-ResponsiveAux/IAAGene Family inAegilops tauschii

2014 ◽  
Vol 40 (12) ◽  
pp. 2059
Author(s):  
Lin-Yi QIAO ◽  
Xin LI ◽  
Zhi-Jian CHANG ◽  
Xiao-Jun ZHANG ◽  
Hai-Xian ZHAN ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Chromosome Location
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