Microarry manifest file annotation

Question

[MOJ]

Can I annotate Illumina's Microarray manifest of file (GSA)? I tried with following steps: 1. Download Clinvar FTP from UCSC 2. Parse GSA file with the downloaded file. Kindly, let me know the feedback on the same

I have also tried with SNPnexus. But could not since SNPnexus accepts only 100,000 SNPs in one go and takes hell tot of time.

[Kevin Blighe]

Hello, can you please describe the data that you currently have, and what you want to add to it? It seems that you want to add ClinVar variant information to your Illumina annotation?

[MOJ]

I have .bpm file. The file contains following heading.

IlmnID Name IlmnStrand SNP AddressA_ID AlleleA_ProbeSeq AddressB_ID AlleleB_ProbeSeq GenomeBuild Chr MapInfo Ploidy Species Source SourceVersion SourceStrand SourceSeq TopGenomicSeq BeadSetID Exp_Clusters Intensity_Only RefStrand 1:103380393-0_B_R_2346041316 1:103380393 BOT [T/C] 94724281 AATAAACTTTTATGCAAAACTTGTAAGATAACTCTTCTTTCCTTCTTCTT 37 1 103380393 diploid Homo sapiens 1000genomes 0 TOP GCTTCCCCTTTCTCTCCTCTTTCTCCTTTGGGACCCTAAACAATGTTAAAAAAAAAAAAA[A/G]AAGAAGAAGGAAAGAAGAGTTATCTTACAAGTTTTGCATAAAAGTTTATTAACCTTGGCA GCTTCCCCTTTCTCTCCTCTTTCTCCTTTGGGACCCTAAACAATGTTAAAAAAAAAAAAA[A/G]AAGAAGAAGGAAAGAAGAGTTATCTTACAAGTTTTGCATAAAAGTTTATTAACCTTGGCA 1355 3 0 - 1:109439680-0_T_F_2348625138 1:109439680 TOP [A/G] 95666109 GTTGGGCAATGCTTATTTCTATTTGCATGATTATGCCAAAGCATTAGAAT 37 1 109439680 diploid Homo sapiens 1000genomes 0 TOP TTTACAGCCAGTTGGGCAATGCTTATTTCTATTTGCATGATTATGCCAAAGCATTAGAAT[A/G]TCACCATCATGATTTAACCCTTGCAAGGTAATTAATTTAAGCTTTTAAATATTCTTCCTT TTTACAGCCAGTTGGGCAATGCTTATTTCTATTTGCATGATTATGCCAAAGCATTAGAAT[A/G]TCACCATCATGATTTAACCCTTGCAAGGTAATTAATTTAAGCTTTTAAATATTCTTCCTT 1382 3 0 + 1:118227370-0_T_R_2346041384 1:118227370 TOP [A/G] 78807930 GAAAATGCATACCCTGCCTTAAAACATTGTTTTTCTAAAAATCCTGTTCT 37 1 118227370 diploid Homo sapiens 1000genomes 0 BOT GTGGCCTGAGGGCCAAATAAGGCAAACAGAttttttttttttttttttttttttttAGTT[T/C]AGAACAGGATTTTTAGAAAAACAATGTTTTAAGGCAGGGTATGCATTTTCCAATTGTCAC GTGACAATTGGAAAATGCATACCCTGCCTTAAAACATTGTTTTTCTAAAAATCCTGTTCT[A/G]AACTaaaaaaaaaaaaaaaaaaaaaaaaaaTCTGTTTGCCTTATTTGGCCCTCAGGCCAC 1355 3 0 -

It is manifest file used to analyse microarray data with GenomeStudio. The file has all the information except rsid annotation with disease/condition. Hence, want to do the same.

[Kevin Blighe]

You could try to annotate these within R by using biomaRt, with an example being here:

• A: How to retrieve Gene name from SNP ID using biomaRt

You will have to develop my code to suit your own situation, though.