Jonathan Keats, PhD 🇨🇦
@pedalheadphx.bsky.social
🇨🇦 boiling in the Arizona desert and not riding my bikes enough. Cancer researcher focused on multiple myeloma and clinical genomics at TGen, part of City of Hope. Creator of MyelomaSky and Sequencing Tech feeds. Director, Collaborative Sequencing Center
Reposted by Jonathan Keats, PhD 🇨🇦
In Solexa days the Illumina software had annotations with this issue on each even chromosome because the two member team had split the effort by chromosome. If I had one superpower it would be to wipe BED files off the face of the earth, don’t care that math works better, not worth the anxiety
November 27, 2025 at 3:20 PM
In Solexa days the Illumina software had annotations with this issue on each even chromosome because the two member team had split the effort by chromosome. If I had one superpower it would be to wipe BED files off the face of the earth, don’t care that math works better, not worth the anxiety
Is there a specific value for CPM versus TPM for comparing a gene between samples? Seems to me that CPM<TPM unless it’s CPM of a UMI/gene. And TPM can do this as well
November 18, 2025 at 3:07 PM
Is there a specific value for CPM versus TPM for comparing a gene between samples? Seems to me that CPM<TPM unless it’s CPM of a UMI/gene. And TPM can do this as well
Things change fast the new IMS/IMWG consensus guidelines no longer consider t(4;14) alone as high risk
New guidelines for high risk
del(17p13)
TP53 mutation
Bi-allelic CDKN2C deletion
1q21 gain AND 1p32 deletion
t(4;14) OR t(14;16) OR t(14;20) AND 1q21 gain OR 1p32 deletion
New guidelines for high risk
del(17p13)
TP53 mutation
Bi-allelic CDKN2C deletion
1q21 gain AND 1p32 deletion
t(4;14) OR t(14;16) OR t(14;20) AND 1q21 gain OR 1p32 deletion
November 14, 2025 at 2:46 PM
Things change fast the new IMS/IMWG consensus guidelines no longer consider t(4;14) alone as high risk
New guidelines for high risk
del(17p13)
TP53 mutation
Bi-allelic CDKN2C deletion
1q21 gain AND 1p32 deletion
t(4;14) OR t(14;16) OR t(14;20) AND 1q21 gain OR 1p32 deletion
New guidelines for high risk
del(17p13)
TP53 mutation
Bi-allelic CDKN2C deletion
1q21 gain AND 1p32 deletion
t(4;14) OR t(14;16) OR t(14;20) AND 1q21 gain OR 1p32 deletion
For it to work you need high molecular weight DNA going in. But it is a very easy prep, just load DNA on the cartridge, hope the workflow gets deployed to the Dragen appliances on the NovaSeq X
October 22, 2025 at 3:51 PM
For it to work you need high molecular weight DNA going in. But it is a very easy prep, just load DNA on the cartridge, hope the workflow gets deployed to the Dragen appliances on the NovaSeq X
Lots of very good treatments available today. Try to get to a center with a myeloma specialist if possible. Easiest suggestion without knowing location is to find the closest NCI designated comprehensive cancer center. The @imfmyeloma.bsky.social and @themmrf.bsky.social have good resources
October 9, 2025 at 6:07 PM
Lots of very good treatments available today. Try to get to a center with a myeloma specialist if possible. Easiest suggestion without knowing location is to find the closest NCI designated comprehensive cancer center. The @imfmyeloma.bsky.social and @themmrf.bsky.social have good resources