PMC:4570283 / 4067-5677
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4570283","sourcedb":"PMC","sourceid":"4570283","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4570283","text":"DNA Samples and Genotyping\nThe Kalash samples were collected from three valleys in the Hindu Kush mountain ranges in northwest Pakistan (Figure 1A). In accordance with the Declaration of Helsinki, the samples were collected after informed consent was obtained, and the study was approved by all relevant institutional ethics committees. Lymphoblastoid cell lines were established from all collected blood samples, and some (n = 25) were deposited with CEPH; these latter samples form part of the South and Central Asian collection of the HGDP-CEPH cell-line panel. We used 10 of these and an additional 13 samples that are not in the collection for our analysis. All of these unrelated (n = 23) Kalash males were genotyped on the Illumina HumanOmni2.5M-8 BeadChip with 200 ng of DNA (26 ng/μl) prepared from these lymphoblastoid cell lines.2 Genotyping calls and quality control (QC) were performed with GenoSNP9 by the Sanger Institute’s core genotyping facility. Genotypes were called only for samples passing Sequenom genetic fingerprinting and gender concordance. These were run through the standard QC pipeline. All 23 samples passed a call-rate threshold of 95% and were used in the downstream analysis. Genotyping quality was assessed by comparison of 178,072 SNPs that overlapped the Illumina 650,000 K SNP chip.5 Ten of the Kalash samples analyzed in this study had also been genotyped on this platform, and the sample genotype concordance was 99.999%. Comparative data were obtained from 35 populations representing Africa, Europe, Caucasus, and West, Central, East, and South Asia (Table S1).5,10–12","divisions":[{"label":"title","span":{"begin":0,"end":26}}],"tracks":[{"project":"2_test","denotations":[{"id":"25937445-11954565-2051072","span":{"begin":840,"end":841},"obj":"11954565"},{"id":"25937445-18653518-2051073","span":{"begin":911,"end":912},"obj":"18653518"},{"id":"25937445-18292342-2051074","span":{"begin":1320,"end":1321},"obj":"18292342"},{"id":"25937445-18292342-2051075","span":{"begin":1608,"end":1610},"obj":"18292342"},{"id":"25937445-24513612-2051075","span":{"begin":1608,"end":1610},"obj":"24513612"},{"id":"25937445-21917723-2051075","span":{"begin":1608,"end":1610},"obj":"21917723"},{"id":"25937445-20531471-2051075","span":{"begin":1608,"end":1610},"obj":"20531471"}],"attributes":[{"subj":"25937445-11954565-2051072","pred":"source","obj":"2_test"},{"subj":"25937445-18653518-2051073","pred":"source","obj":"2_test"},{"subj":"25937445-18292342-2051074","pred":"source","obj":"2_test"},{"subj":"25937445-18292342-2051075","pred":"source","obj":"2_test"},{"subj":"25937445-24513612-2051075","pred":"source","obj":"2_test"},{"subj":"25937445-21917723-2051075","pred":"source","obj":"2_test"},{"subj":"25937445-20531471-2051075","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecdc93","default":true}]}]}}