|
| Status |
Public on May 01, 2021 |
| Title |
liverTissue_genotypes_sample_SJLB670 |
| Sample type |
genomic |
| |
|
| Source name |
liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
age: 49
tissue: liver
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard Illumina protocol
|
| Label |
Cy5, Cy3
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Description |
The 'SJLB' prefix stands for 'ST. Jude liver bank' and is prepended to sample IDs in the .idat and .vcf files. The 'SJLB' prefix is removed from sample IDs in the manuscript to save space.
|
| Data processing |
We mapped the Illumina array probe sequences to the hg19 genome assembly using novoalign, excluding variants with ambiguous probe alignments and variants with 1000 Genomes (1000G) phase 3 minor allele frequency (MAF) >.01 within 7 bp of the 3’ end of probes. No individuals were related at a 3rd-degree relationship threshold using KING v1.4. Prior to genotype imputation, we combined the genotypes of the samples in this study with genotypes from 177 samples from a separate study genotyped on similar chips and removed variants that met the following criteria: allele frequency difference >20% with 1000G phase 3 Europeans, palindromic variants with MAF>.2, genotype missingness > 2.5%, and extreme deviation from Hardy-Weinberg Equilibrium (p<1x10-4). Using the Michigan Imputation Server, we phased 1,789,889 autosomal variants using Eagle v2.3 and imputed missing genotypes using minimac3 with the Haplotype Reference Consortium (hrc.r1.1.2016) panel. The VCF files contain all imputed variants with imputation r2>.3. However, we restricted to biallelic variants in the manuscript.
|
| |
|
| Submission date |
Jan 15, 2021 |
| Last update date |
May 02, 2021 |
| Contact name |
Karen L Mohlke |
| E-mail(s) |
mohlke@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL25201 |
| Series (2) |
| GSE164938 |
Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes] |
| GSE164942 |
Genetic effects on liver chromatin accessibility identify disease regulatory variants |
|
