[Nelsonlab-analysis] NF2 meningioma copy number from LMP sequence data

[Michael J. C. <mic...@gm...>]

Hi all,
I performed copy number analysis on the LMP sequence data. My approach:

1) Calculated mean coverage for 10kb intervals across the entire genome for
both tumor and germline.
2) Normalized coverage by dividing each 10kb mean coverage interval by whole
genome mean coverage.
3) Calculated log2R-ratio
(normalized-tumor-coverage/normalized-germline-coverage).
4) Used DNAcopy to generate smoothed copy number segments (the black lines
on each chart).

The results: 
http://genomics.ctrl.ucla.edu/~mclark/HEI_NF2/HEI.coverage-derived.copy.numb
er.png

Chromosome 22 loss is evident, which Benedicte saw with MLPA as well.
Smoothed log2R-ratio of chr22 is at -0.3.
Across the non-centromeric length of all other chromosomes, smoothed
log2R-ratio is at or below +/-0.1, suggesting no other major losses or gains
in the genome.

There are some smaller events. I¹m going to run this again using 1kb
intervals in the interest of better identifying those small events.

Mike