Infinium Global Screening Array-Why there are few rsids/chromosome positons with more than one loci on the chip?

Question

[rekha0912]

Hi All,

I am using Illumina's Infinium Global Screening Array and processing the data in GenomeStudio. Now, in the manifest file(GSAMD-24v1-0_20011747_A1.bpm or GSAMD-24v1-0_20011747_A1.csv), it has been observed that some rsids are repeated with little modification to the Ilumina ID. Also, these repeat loci have the same chromosome location. Below I have mentioned one such example for rs12248560 (four entries found)-

IlmnID  Name    IlmnStrand  SNP

chr10-96521657:rs12248560-AC-0_B_R_2337080012   chr10-96521657:rs12248560-AC    BOT [T/G]
chr10-96521657:rs12248560-TC-0_B_F_2337080013   chr10-96521657:rs12248560-TC    BOT [T/C]

DUP-seq-rs12248560-0_T_R_2348760142 DUP-seq-rs12248560  TOP [A/G]
seq-rs12248560-0_T_R_2344434431 seq-rs12248560  TOP [A/G]

What does it mean? Are these duplicate entries and if yes, which one to consider?

Also, in some patients, genotype for all the four loci have been captured.

Please explain the difference and how to use such data.

Thank you

[rednalf]

Hello. I am also interested in this .csv manifest file. Where can I download this same version?

Answer 1

[ShirleyDai]

I guess these loci are multi-alleles. You can check them in NCBI-SNP.