search

fpbarthel / GLASS

GLASS consortium
MIT License
37 stars 13 forks source link

Unexpected CNV stability in cases sequenced at Dana Farber #128

Closed Kcjohnson closed 5 years ago

Kcjohnson commented 5 years ago

The following samples had flatline CNV profiles:

GLSS-DF-0002-R1|TP
GLSS-DF-0003-R1
GLSS-DF-0004-TP
GLSS-DF-0010-R1
GLSS-DF-0012-R1|TP
GLSS-19-0268-R1-02D (sequenced at DF)
GLSS-19-0271-R1-02D (sequenced at DF)

It seems off that some of these samples would have quite altered genomes at one time point, but nearly unaltered at the other.

Case example with canonical Chr7 gain, Chr10 loss at primary diagnosis. glss-df-0003-tp-01d-wxs-imr04g

Unexpected stability at recurrence, but it still picks up an EGFR amplification. glss-df-0003-r1-01d-wxs-bkukvh

Since this affected more than ~50% of the cases from this dataset we are launching an investigation to find out whether this is a data quality issue (coverage, low purity) or another matter.

Kcjohnson commented 5 years ago

We have not included these aforementioned samples in the gold_set in the GLASS marker paper.