Laboratory Medicine and Quality Assurance

Table. 4.

Results of NGS-based liquid biopsy in 2023

Trials Gene Variant Description No. of labs (%)
1st GNL-23-01 APC (1) Detected c.2557G>T (p.Glu853*) 4 (44.4)
c.2557G>T (p.Glu853Ter) 4 (44.4)
c.2557G>T(p.Glu853Ter) 1 (11.1)
APC (2) Detected c.5947G>T (p.Glu1983*) 4 (44.4)
c.5947G>T (p.Glu1983Ter) 4 (44.4)
c.5947G>T(p.Glu1983Ter) 1 (11.1)
BRAF Detected c.1799T>A (p.Val600Glu) 10 (83.3)
c.1799T>A(p.Val600Glu) 1 (8.3)
c.1799T>A (p.V600E) 1 (8.3)
CDKN2A (1) Not detected - 9 (100.0)
CDKN2A (2) Not detected - 9 (100.0)
CTNNB1 Not detected - 9 (100.0)
EGFR (1) Detected c.2236_2250del (p.Glu746_Ala750del) 10 (83.3)
c.2236_2250del(p.Glu746_Ala750del) 1 (8.3)
c.2236_2250delGAATTAAGAGAAGCA (p.E746_A750del) 1 (8.3)
EGFR (2) Not detected - 12 (100.0)
EGFR (3) Detected c.2573T>G (p.Leu858Arg) 10 (83.3)
c.2573T>G(p.Leu858Arg) 1 (8.3)
c.2573T>G (p.L858R) 1 (8.3)
FGFR1 Not detected - 9 (100.0)
FGFR3 Not detected - 9 (100.0)
FLT3 Detected c.969C>A (p.Asn323Lys) 8 (88.9)
c.969C>A(p.Asn323Lys) 1 (11.1)
KIT Not detected - 9 (100.0)
KRAS Detected c.34G>A (p.Gly12Ser) 10 (83.3)
c.34G>A(p.Gly12Ser) 1 (8.3)
c.34G>A (p.G12S) 1 (8.3)
MLH1 Not detected - 9 (100.0)
MSH2 Detected c.1168C>T (p.Leu390Phe) 7 (87.5)
c.1168C>T(p.Leu390Phe) 1 (12.5)
NF2 Detected c.385G>T (p.Glu129*) 4 (44.4)
c.385G>T (p.Glu129Ter) 4 (44.4)
c.385G>T(p.Glu129Ter) 1 (11.1)
PALB2 Detected c.1676A>G (p.Gln559Arg) 7 (87.5)
c.1676A>G(p.Gln559Arg) 1 (12.5)
Not detected - 1 (11.1)
PIK3CA (1) Not detected - 12 (100.0)
PIK3CA (2) Detected c.1345C>A (p.Pro449Thr) 10 (90.9)
c.1345C>A(p.Pro449Thr) 1 (9.1)
STK11 (1) Detected c.109C>T (p.Gln37*) 4 (44.4)
c.109C>T (p.Gln37Ter) 4 (44.4)
c.109C>T(p.Gln37Ter) 1 (11.1)
STK11 (2) Detected c.647C>T (p.Ser216Phe) 8 (88.9)
c.647C>T(p.Ser216Phe) 1 (11.1)
TP53 (1) Detected c.818G>A (p.Arg273His) 10 (83.3)
c.818G>A(p.Arg273His) 1 (8.3)
c.818G>A (p.R273H) 1 (8.3)
TP53 (2) Not detected - 12 (100.0)
TP53 (3) Detected c.742C>G (p.Arg248Gly) 10 (83.3)
c.742C>G(p.Arg248Gly) 1 (8.3)
c.742C>G (p.R248G) 1 (8.3)
TP53 (4) Detected c.560-1G>A (p.?) 8 (66.7)
c.560-1G>A 3 (25.0)
c.560-1G>A(p.?) 1 (8.3)
1st GNL-23-02 APC (1) Not detected - 9 (100.0)
APC (2) Not detected - 9 (100.0)
BRAF Not detected - 12 (100.0)
CDKN2A (1) Detected c.205G>T (p.Glu69*) 4 (44.4)
c.205G>T (p.Glu69Ter) 4 (44.4)
c.205G>T(p.Glu69Ter) 1 (11.1)
CDKN2A (2) Detected c.200G>T (p.Gly67Val) 8 (88.9)
c.200G>T(p.Gly67Val) 1 (11.1)
CTNNB1 Detected c.223A>G (p.Thr75Ala) 8 (88.9)
c.223A>G(p.Thr75Ala) 1 (11.1)
EGFR (1) Detected c.2235_2249del (p.Glu746_Ala750del) 10 (83.3)
c.2235_2249del(p.Glu746_Ala750del) 1 (8.3)
c.2235_2249delGGAATTAAGAGAAGC (p.E746_A750del) 1 (8.3)
EGFR (2) Detected c.2369C>T (p.Thr790Met) 10 (83.3)
c.2369C>T(p.Thr790Met) 1 (8.3)
c.2573T>G (p.Leu858Arg) 10 (83.3)
EGFR (3) Detected c.2573T>G(p.Leu858Arg) 1 (8.3)
c.2369C>T (p.T790M) 1 (8.3)
c.2573T>G (p.L858R) 1 (8.3)
FGFR1 Detected c.626G>A (p.Arg209His) 7 (77.8)
c.626G>A(p.Arg209His) 1 (11.1)
c.719G>A (p.Arg240His) 1 (11.1)
FGFR3 Detected c.101G>A (p.Arg34Gln) 8 (88.9)
c.101G>A(p.Arg34Gln) 1 (11.1)
FLT3 Not detected - 9 (100.0)
KIT Detected c.878A>G (p.Asn293Ser) 7 (87.5)
c.878A>G(p.Asn293Ser) 1 (12.5)
KRAS Detected c.34G>T (p.Gly12Cys) 10 (83.3)
c.34G>T(p.Gly12Cys) 1 (8.3)
c.34G>T (p.G12C) 1 (8.3)
MLH1 Detected c.311del (p.Leu104TrpfsTer4) 5 (55.6)
c.311del (p.Leu104Trpfs*4) 3 (33.3)
c.311del(p.Leu104TrpfsTer4) 1 (11.1)
MSH2 Not detected - 9 (100.0)
NF2 Not detected - 9 (100.0)
PALB2 Detected c.1676A>G (p.Gln559Arg) 7 (87.5)
c.1676A>G(p.Gln559Arg) 1 (12.5)
Not detected - 1 (11.1)
PIK3CA (1) Detected c.353G>A (p.Gly118Asp) 10 (83.3)
c.353G>A(p.Gly118Asp) 1 (8.3)
c.353G>A (p.G118D) 1 (8.3)
PIK3CA (2) Not detected - 11 (100.0)
STK11 (1) Not detected - 9 (100.0)
STK11 (2) Not detected - 9 (100.0)
TP53 (1) Detected c.818G>A (p.Arg273His) 10 (83.3)
c.818G>A(p.Arg273His) 1 (8.3)
c.818G>A (p.R273H) 1 (8.3)
TP53 (2) Detected c.743G>A (p.Arg248Gln) 10 (83.3)
c.743G>A(p.Arg248Gln) 1 (8.3)
c.743G>A (p.R248Q) 1 (8.3)
TP53 (3) Not detected - 12 (100.0)
TP53 (4) Not detected - 12 (100.0)
2nd GNL-23-03 APC Detected c.5947G>T (p.Glu1983Ter) 6 (66.7)
c.5947G>T (p.Glu1983*) 3 (33.3)
BRAF Detected c.1799T>A (p.Val600Glu) 10 (90.9)
c.1799T>A (p.V600E) 1 (9.1)
CDKN2A (1) Not detected - 9 (100.0)
CDKN2A (2) Not detected - 9 (100.0)
EGFR (1) Detected c.2236_2250del (p.Glu746_Ala750del) 10 (90.9)
c.2236_2250delGAATTAAGAGAAGCA (p.E746_A750del) 1 (9.1)
EGFR (2) Not detected - 11 (100.0)
EGFR (3) Not detected - 11 (100.0)
FLT3 Detected c.969C>A (p.Asn323Lys) 8 (88.9)
Not detected - 1 (11.1)
KIT Not detected - 9 (100.0)
KRAS Detected c.34G>A (p.Gly12Ser) 10 (90.9)
c.34G>A (p.G12S) 1 (9.1)
MLH1 Not detected - 9 (100.0)
MSH2 (1) Detected c.1168C>T (p.Leu390Phe) 9 (100.0)
MSH2 (2) Detected c.1786_1799delinsT (p.Asn596PhefsTer3) 6 (66.7)
c.1786_1799delinsT (p.Asn596Phefs*3) 2 (22.2)
Not detected - 1 (11.1)
NF2 Detected c.385G>T (p.Glu129Ter) 6 (66.7)
c.385G>T (p.Glu129*) 3 (33.3)
NRAS (1) Not detected - 11 (100.0)
NRAS (2) Detected c.181C>A (p.Gln61Lys) 10 (90.9)
c.181C>A (p.Q61K) 1 (9.1)
PALB2 Detected c.1676A>G (p.Gln559Arg) 9 (100.0)
PIK3CA Not detected - 11 (100.0)
STK11 (1) Detected c.109C>T (p.Gln37Ter) 6 (66.7)
c.109C>T (p.Gln37*) 3 (33.3)
STK11 (2) Detected c.647C>T (p.Ser216Phe) 9 (100.0)
TP53 (1) Not detected - 11 (100.0)
TP53 (2) Not detected - 11 (100.0)
TP53 (3) Detected c.742C>G (p.Arg248Gly) 10 (90.9)
c.742C>G (p.R248G) 1 (9.1)
TP53 (4) Not detected - 9 (100.0)
2nd GNL-23-04 APC Not detected - 9 (100.0)
BRAF Not detected - 11 (100.0)
CDKN2A (1) Detected c.205G>T (p.Glu69Ter) 6 (66.7)
c.205G>T (p.Glu69*) 3 (33.3)
CDKN2A (2) Detected c.200G>T (p.Gly67Val) 9 (100.0)
EGFR (1) Detected c.2235_2249del (p.Glu746_Ala750del) 10 (90.9)
c.2235_2249delGGAATTAAGAGAAGC (p.E746_A750del) 1 (9.1)
EGFR (2) Detected c.2369C>T (p.Thr790Met) 10 (90.9)
c.2369C>T (p.T790M) 1 (9.1)
EGFR (3) Detected c.2573T>G (p.Leu858Arg) 10 (90.9)
c.2573T>G (p.L858R) 1 (9.1)
FLT3 Not detected - 9 (100.0)
KIT Detected c.878A>G (p.Asn293Ser) 9 (100.0)
KRAS Not detected - 11 (100.0)
MLH1 Detected c.311del (p.Leu104TrpfsTer4) 6 (66.7)
c.311del (p.Leu104Trpfs*4) 3 (33.3)
MSH2 (1) Not detected - 9 (100.0)
MSH2 (2) Not detected - 9 (100.0)
NF2 Not detected - 9 (100.0)
NRAS (1) Detected c.182A>G (p.Gln61Arg) 10 (90.9)
c.182A>G (p.Q61R) 1 (9.1)
NRAS (2) Not detected - 11 (100.0)
PALB2 Detected c.1676A>G (p.Gln559Arg) 9 (100.0)
PIK3CA Detected c.353G>A (p.Gly118Asp) 10 (90.9)
c.353G>A (p.G118D) 1 (9.1)
STK11 (1) Not detected - 9 (100.0)
STK11 (2) Not detected - 9 (100.0)
TP53 (1) Detected c.818G>A (p.Arg273His) 10 (90.9)
c.818G>A (p.R273H) 1 (9.1)
TP53 (2) Detected c.743G>A (p.Arg248Gln) 10 (90.9)
743G>A (p.R248Q) 1 (9.1)
TP53 (3) Not detected - 11 (100.0)
TP53 (4) Detected c.375G>A (p.Thr125=) 9 (100.0)

Bold lettering indicates results that are not compliant with the intended responses.

Abbreviation: NGS, next-generation sequencing.

Lab Med Qual Assur 2024;46:115~129 https://doi.org/10.15263/jlmqa.2024.46.3.115
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