Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling
| Autor: | Jason A. Reuter, Reetesh K. Pai, Michael Snyder, Damek V. Spacek |
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| Rok vydání: | 2016 |
| Předmět: |
Male
0301 basic medicine Cancer genome sequencing Esophageal Neoplasms Kinesins Transposases Genomics Biology Biochemistry Genome Article Germline Transcriptome 03 medical and health sciences chemistry.chemical_compound medicine Humans RNA Messenger Molecular Biology Gene Library Genetics Genome Human Sequence Analysis RNA Gene Expression Profiling RNA Cancer DNA Sequence Analysis DNA Cell Biology medicine.disease 030104 developmental biology chemistry Mutation Biotechnology |
| Zdroj: | Nature methods |
| ISSN: | 1548-7105 1548-7091 |
| DOI: | 10.1038/nmeth.4028 |
| Popis: | Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. here, we introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. We apply the method to laser-capture-microdissected esophageal adenocarcinoma tissue, revealing a highly aneuploid tumor genome with extensive blocks of increased homozygosity and corresponding increases in allele-specific expression. Among this widespread allele-specific expression, we identify germline polymorphisms that are associated with response to cancer therapies. We further leverage this integrative data to uncover expressed mutations in several known cancer genes as well as a recurrent mutation in the motor domain of KIF3B that significantly affects kinesin–microtubule interactions. Simul-seq provides a new streamlined approach for generating comprehensive genome and transcriptome profiles from limited quantities of clinically relevant samples. |
| Databáze: | OpenAIRE |
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