Information regarding genotype calling at Dartmouth can be found here.
This list has the strands the TOP alleles from the Oncoarray chip refer to. Most strands were determined by blasting the probe sequence against 1KG sequencing. Some unknown strands were changed to reflect the alleles of the 1KG variant matched to the SNP. Some ambiguous SNPs were flipped to match the expected frequency of the 1KG. Some positions for SNPs with rs numbers were updated to match dbSNP and the probe sequence was confirmed to be in the amended position. The positions for Indels matched to 1KG variants have been amended to match the 1KG system of numbering (i.e. one less than the manifest position.)
The SNPs that have been matched to 1KG variants and their alleles are listed in this file.
Descriptions of retrieving your requesting markers in OncoArray data can be found here.
The List of Probe Sequences can be found in this file here
The QC process is documented here.
The number of SNPs excluded at each step is summarized in this file.
There are a number of variants on the chip with the same probe in the same position (or a few with the same alleles but the sequence from the opposite strand.) The probe with the worse QC scores and call rate is chosen for exclusion.
For checking the sex of samples use the 300 Y markers confirmed to work in males and to have a non-autosomal pattern in their cluster plots, seen in this list. In addition chromosome X SNPs that have many heterozygous calls in males and/or autosomal cluster plots should be not be used for sex checks.
The list used in Cambridge of 49,659 SNPs to exclude before producing imputation input files is available.
Duplicate report for samples from the Lung and Head and Neck Oncoarray project.