Question: Custom exome array chip with 527 SNPs have chromosome information with 0
gravatar for aydzhouyuan
6.0 years ago by
aydzhouyuan20 wrote:

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?






snp • 2.3k views
ADD COMMENTlink modified 4.1 years ago by Matt Shirley9.3k • written 6.0 years ago by aydzhouyuan20
gravatar for Maxime Lamontagne
5.9 years ago by
Maxime Lamontagne2.2k wrote:

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.

ADD COMMENTlink written 5.9 years ago by Maxime Lamontagne2.2k
gravatar for mariaf.betancur
4.1 years ago by
mariaf.betancur0 wrote:

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

ADD COMMENTlink written 4.1 years ago by mariaf.betancur0
gravatar for Matt Shirley
4.1 years ago by
Matt Shirley9.3k
Cambridge, MA
Matt Shirley9.3k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Matt Shirley9.3k
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