Molecular pattern of ven/aza relapse measured by clinical NGS and ddPCR
Analyzed by Shanshan Pei
10 June, 2020
Update notes
06/10/20
In response to Amanda’s email on 5/27/20 and 5/29/20
1. Comments from the NGS and the ddPCR sheets are now printed under each plot per HTB patient
2. A * notation for “Priority” have been given to HTB patients that are of higher priority
3. HTB-1434, a new paitent is added, ngs data is updated, ddpcr data is pending…
4. For HTB-1390 (Lalone), in the NGS sheet, i have moved the information (yes, and 67%) from the FLT3.Y597_E598ins16 column to the FLT3-ITD column.
05/25/20
In repsonse to Amanda’s email on 5/22/20, following updates are made:
1. Removal of
ASXL1 E1102D (HTB-719 and HTB-1011)
TET2 P363L (HTB-691)
BCORL1 N1302K (HTB-719) ***Note: I think that you are actually referring to N1382K.
RUNX1 L29S (HTB-691)
ASXL1 P675fs (HTB-719)
2. Now using DNMT3A.F731fs to replace DNMT3A.542_543del in HTB-691
3. Removal of BCOR S1431Y from HTB-SK001.
4. KRAS.G13A is now fixed as KRAS.G12A for HTB-956
Detailed responses in my email back to Amanda on 5/25/20.
Results
## [1] "HTB-1261"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-12-22 " "Rl 2018-12-13 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-12-22 missing SMC1A x 2 (assays ordered)"
## [2] "MRD 2018-01-26 "
## [3] " 2018-05-01 "
## [4] " 2018-07-24 "
## [5] " 2018-09-28 "
## [6] "Rl 2018-12-13 "
## [1] "HTB-1387"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-08-14 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2018-08-14 " " 2018-08-24 "
## [3] "MRD 2018-09-13 ddPCR from 9/13/2018" " 2018-10-25 "
## [5] " 2019-02-26 " " 2019-04-02 "
## [7] "Rl 2019-04-30 "
## [1] "HTB-1434"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-10-12 TET2 L1229R 87% (possibly germline, but fingernails were inconclusive)"
## [2] "Rl 2020-05-07 "
## [1] "================ddPCR notes by AW ==========================="
## character(0)
## [1] "HTB-1493"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2019-01-16 " "Rl 2019-04-30 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2019-01-16 ddPCR completed"
## [2] " 2019-01-24 "
## [3] " 2019-02-14 "
## [4] "MRD 2019-03-26 2.4% Hematologics MRD pos"
## [5] "Rl 2019-04-30 "
## [1] "HTB-691"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2016-04-21 " "Rl 2018-11-07 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2016-04-21 " "MRD 2016-05-23 " " 2016-08-15 " " 2016-11-07 "
## [5] " 2017-02-03 " " 2017-07-24 " " 2018-01-02 " " 2018-06-27 "
## [9] "Rl 2018-11-07 "
## [1] "HTB-719"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2016-05-19 " "Rl 2020-01-16 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "MRD 2016-07-01 " " 2016-10-04 " " 2017-01-09 " " 2017-04-13 "
## [5] " 2017-10-10 " " 2018-04-03 " " 2019-03-21 " " 2019-09-17 "
## [9] "Rl 2020-01-16 "
## [1] "HTB-956"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-04-03 " "Rl 2019-07-17 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-04-03 missing KRAS (ordered) and TET2 x 2"
## [2] "MRD 2017-05-02 "
## [3] " 2017-08-17 "
## [4] " 2017-09-19 "
## [5] " 2018-01-02 "
## [6] " 2018-03-08 "
## [7] " 2018-05-24 "
## [8] " 2018-11-29 "
## [9] " 2019-04-04 "
## [10] "Rl 2019-07-17 "
## [1] "HTB-998"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-03-22 " "Rl 2017-10-05 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-03-22 missing DNMT3A (assay TBD)"
## [2] " 2017-04-20 "
## [3] "MRD 2017-05-23 "
## [4] " 2017-07-13 "
## [5] "Rl 2017-10-05 "
## [1] "HTB-SK001"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2016-08-19 " "Rl 2017-11-30 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2016-08-09 BCOR S1431Y suspected germline; otherwise ddPCR done"
## [2] "MRD 2016-09-13 "
## [3] " 2016-10-27 "
## [4] " 2017-05-15 "
## [5] " 2017-07-06 "
## [6] " 2017-09-29 "
## [7] "Rl 2017-11-30 "
## [1] "HTB-1009"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-04-05 " "Rl 2019-05-30 "
## [1] "================ddPCR notes by AW ==========================="
## character(0)
## [1] "HTB-1011"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-03-31 " "Rl 2017-11-15 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-03-31 missing DNMT3A fs (assay TBD)"
## [2] "MRD 2017-05-08 "
## [3] " 2017-08-14 "
## [4] "Rl 2017-11-15 "
## [1] "HTB-1257"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-12-18 " "Rl 2018-11-01 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-12-18 " " 2018-02-06 "
## [3] "MRD 2018-03-08 " " 2018-03-22 "
## [5] " 2018-06-14 " "Rl 2018-11-01 ddPCR done 12/20/2018"
## [1] "HTB-1259"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-12-21 " "Rl 2018-12-18 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-12-21 missing relapse sample"
## [2] "MRD 2018-02-08 "
## [3] " 2018-05-21 "
## [4] " 2018-08-06 "
## [1] "HTB-1350"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-05-29 " "Rl 2018-11-12 "
## [1] "================ddPCR notes by AW ==========================="
## character(0)
## [1] "HTB-1390"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-08-20 " "Rl 2019-02-21 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2018-08-20 FLT3 is ITD, VAF unknown from diagnosis"
## [2] " 2018-08-30 "
## [3] " 2018-09-20 "
## [4] "MRD 2018-10-30 "
## [5] " 2018-12-06 "
## [6] "Rl 2019-02-21 "
## [1] "HTB-1467"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-11-28 " "Rl 2019-01-31 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2018-11-28 attempted KMT2A, assay failed"
## [2] " 2018-12-13 "
## [3] "MRD 2018-12-27 "
## [4] "Rl 2019-01-31 "
## [1] "HTB-1471"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-12-05 " "Rl 2019-07-11 "
## [1] "================ddPCR notes by AW ==========================="
## character(0)
## [1] "HTB-1513"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2019-04-15 " "Rl 2019-08-12 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2019-04-15 missing relapse sample"
## [2] " 2019-05-06 "
## [3] "MRD 2019-05-20 "
## [1] "HTB-1591"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2019-06-20 " "Rl 2019-12-09 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2019-06-20 low priority, no changes in VAFs"
## [2] "Rl 2019-12-09 ddPCR from 12/19/2019"
## [1] "HTB-368"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-05-17 " "Rl 2019-04-04 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2018-05-17 ddPCR completed" " 2018-05-29 "
## [3] "MRD 2018-06-19 " " 2018-07-26 "
## [5] " 2018-09-04 " " 2018-11-27 "
## [7] " 2019-01-29 " "Rl 2019-04-04 "
## [1] "HTB-483"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2015-02-12 IDH1 synonymous mutation rs11554137"
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2015-02-12 only PB available" "MRD 2015-04-02 only PB available"
## [3] "Rl 2015-08-28 only PB available"
## [1] "HTB-935"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-01-17 " "Rl 2020-01-14 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-01-17 missing relapse sample"
## [2] "MRD 2017-02-23 "
## [3] " 2017-06-13 "
## [4] " 2017-09-07 "
## [5] "Rl 2020-01-14 "
## [1] "HTB-970"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-02-22 " "Rl 2017-10-06 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-02-22 TET2 x 2 low priority (no changes)"
## [2] "MRD 2017-04-06 "
## [3] " 2017-07-20 "
## [4] "Rl 2017-10-06 "
## [1] "HTB-976"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2017-04-11 " "Rl 2017-11-29 "
## [1] "================ddPCR notes by AW ==========================="
## [1] "Dx 2017-04-11 ddPCR done" "MRD 2017-05-15 "
## [3] " 2017-08-21 " "Rl 2017-11-29 "
## [1] "HTB-NOTB_CL"
## [1] "=================NGS notes by SSP ==========================="
## [1] "Dx 2018-10-15 "
## [1] "================ddPCR notes by AW ==========================="
## character(0)