Custom exome array chip with 527 SNPs have chromosome information with 0

Question

[aydzhouyuan]

Dear All

I am now cleaning the illumina custom MS exome array chip (about 330k SNPs). Basically, I import the raw data into Genomestudio, recluster and import data into Plink format. All the sample genotype call rate (>98%). However, I found in the bim file, 527 SNPs with the first column(chromosome information) marked as 0. I am confused what does this mean? why would this happen? see below example

0    MS_Replication_Chip_chr1-reichrank1555    0    993    0    G

Also I found we have about 150k SNPs are monomorhic, is this correct?

Any one have any suggestions?

Thanks

[mariaf.betancur]

Did you able to find out answer for this ? I have the same problem, I don’t know what happened

Answer 1

[Maxime Lamontagne]

If your chip was design a few years ago, some SNPs are discontinued or change name. Maybe Genomestudio put chr=0 because they do not map to the human genome anymore.

150k mono: How many samples do you have? It could explain this situation.

Answer 2

[Matt Shirley]

It's likely that those probes are actually control sequences used to QC the chip during development or production. It's been while since I worked with SNP chip data, but there were always a few probes that don't target human/mouse/whatever, and so those will be excluded from analysis. You should be able to distinguish them by their probe ID.