Laboratory Medicine and Quality Assurance

Table. 1.

Results of NGS-based liquid biopsy in 2020

Trials Gene Variant Description No. of labs (%)
1st GNL-20-01 BRAF Detected NM_004333.4(BRAF):c.1799T>A (p.Val600Glu) 2 (50.0)
NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) 1 (25.0)
c.1799T>A, p.Val600Glu 1 (25.0)
EGFR (1) Detected NM_005228.3(EGFR):c.2235_2249del (p.Glu746_Ala750del) 1 (25.0)
NM_005228.5(EGFR):c.2235_2249del15 (p.Glu746_Ala750del) 1 (25.0)
NM_005228.5(EGFR):c.2235_2249delGGAATTAAGAGAAGC (p.Glu746_Ala750del) 1 (25.0)
c.2235_2249del, p.Glu746_Ala750del 1 (25.0)
EGFR (2) Detected c.2300_2308dup, p.Ala767_Val769dup 1 (25.0)
NM_005228.3(EGFR):c.2300_2308dup (p.Ala767_Val769dup) 1 (25.0)
NM_005228.5(EGFR):c.2300_2308dup (p.Ala767_Val769dup) 1 (25.0)
NM_005228.5(EGFR):c.2300_2308dupTGGCCAGCG (p.Ala767_Val769dup) 1 (25.0)
EGFR (3) Detected NM_005228.5(EGFR):c.2369C>T (p.Thr790Met) 2 (50.0)
NM_005228.3(EGFR):c.2369C>T (p.Thr790Met) 1 (25.0)
c.2369C>T, p.Thr790Met 1 (25.0)
EGFR (4) Detected NM_005228.5(EGFR):c.2573T>G (p.Leu858Arg) 2 (50.0)
NM_005228.3(EGFR):c.2573T>G (p.Leu858Arg) 1 (25.0)
c.2573T>G, p.Leu858Arg 1 (25.0)
KRAS Detected NM_004985.5(KRAS):c.35G>A (p.Gly12Asp) 2 (50.0)
NM_004985.3(KRAS):c.35G>A (p.Gly12Asp) 1 (25.0)
c.35G>A, p.Gly12Asp 1 (25.0)
NRAS (1) Detected NM_002524.5(NRAS):c.181C>A (p.Gln61Lys) 2 (50.0)
NM_002524.4(NRAS):c.181C>A (p.Gln61Lys) 1 (25.0)
c.181C>A, p.Gln61Lys 1 (25.0)
NRAS (2) Detected NM_002524.5(NRAS):c.175G>A (p.Ala59Thr) 2 (50.0)
NM_002524.4(NRAS): c.175G>A (p.Ala59Thr) 1 (25.0)
c.175G>A, p.Ala59Thr 1 (25.0)
PIK3CA Detected NM_006218.4(PIK3CA):c.1633G>A (p.Glu545Lys) 1 (25.0)
NM_006218.2(PIK3CA):c.1633G>A (p.Glu545Lys) 1 (25.0)
c.1633G>A, p.Glu545Lys 1 (25.0)
Not detected - 1 (25.0)
1st GNL-20-02 BRAF Detected NM_004333.4(BRAF):c.1799T>A (p.Val600Glu) 2 (50.0)
NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) 1 (25.0)
c.1799T>A, p.Val600Glu 1 (25.0)
EGFR (1) Detected NM_005228.3(EGFR):c.2235_2249del (p.Glu746_Ala750del) 1 (25.0)
NM_005228.5(EGFR):c.2235_2249del15 (p.Glu746_Ala750del) 1 (25.0)
Not detected - 2 (50.0)
EGFR (2) Not detected - 4 (100.0)
EGFR (3) Detected NM_005228.5(EGFR):c.2369C>T (p.Thr790Met) 1 (25.0)
NM_005228.3(EGFR):c.2369C>T (p.Thr790Met) 1 (25.0)
c.2369C>T, p.Thr790Met 1 (25.0)
Not detected - 1 (25.0)
EGFR (4) Detected c.2573T>G, p.Leu858Arg 1 (25.0)
Not detected - 3 (75.0)
KRAS Detected NM_004985.3(KRAS):c.35G>A (p.Gly12Asp) 1 (25.0)
35G>A, p.Gly12Asp 1 (25.0)
Not detected - 2 (50.0)
NRAS (1) Detected NM_002524.5(NRAS):c.181C>A (p.Gln61Lys) 1 (25.0)
c.181C>A, p.Gln61Lys 1 (25.0)
Not detected - 2 (50.0)
NRAS (2) Detected NM_002524.4(NRAS): c.175G>A (p.Ala59Thr) 1 (25.0)
Not detected - 3 (75.0)
PIK3CA Detected NM_006218.4(PIK3CA):c.1633G>A (p.Glu545Lys) 1 (25.0)
Not detected - 3 (75.0)
2nd GNL-20-03 BRAF Not detected - 4 (100.0)
EGFR (1) Detected NM_005228.5(EGFR):c.2235_2249del (p.Glu746_Ala750del) 2 (50.0)
NM_005228.5(EGFR):c.2235_2249del15 (p.Glu746_Ala750del) 1 (25.0)
NM_005228.5(EGFR):c.2235_2249delGGAATTAAGAGAAGC (p.Glu746_Ala750del) 1 (25.0)
EGFR (2) Not detected - 4 (100.0)
EGFR (3) Detected NM_005228.5(EGFR):c.2573T>G (p.Leu858Arg) 4 (100.0)
KRAS Detected NM_004985.5(KRAS):c.34G>T (p.Gly12Cys) 4 (100.0)
PIK3CA Not detected - 4 (100.0)
TP53 (1) Not detected - 4 (100.0)
TP53 (2) Detected NM_000546.5(TP53):c.743G>A (p.Arg248Gln) 3 (75.0)
NM_000546.6(TP53):c.743G>A (p.Arg248Gln) 1 (25.0)
TP53 (3) Not detected - 4 (100.0)
TP53 (4) Detected NM_000546.5(TP53):c.560-1G>A 2 (50.0)
NM_000546.5(TP53):c.560-1G>A (p.?) 1 (25.0)
NM_000546.5(TP53):c.560-1G>C 1 (25.0)
2nd GNL-20-04 BRAF Detected NM_004333.4(BRAF):c.1799T>A (p.Val600Glu) 3 (75.0)
NM_004333.4(BRAF):c.1799T>A, (p.Val600Glu) 1 (25.0)
EGFR (1) Detected NM_005228.5(EGFR):c.2236_2250del (p.Glu746_Ala750del) 2 (50.0)
NM_005228.5(EGFR):c.2236_2250del15 (p.Glu746_Ala750del) 1 (25.0)
NM_005228.5(EGFR):c.2236_2250delGAATTAAGAGAAGCA (p.Glu746_Ala750del) 1 (25.0)
EGFR (2) Detected NM_005228.5(EGFR):c.2369C>T (p.Thr790Met) 4 (100.0)
EGFR (3) Detected NM_005228.5(EGFR):c.2573T>G (p.Leu858Arg) 3 (75.0)
NM_005228.5(EGFR)c.2573T>G (p.Leu858Arg) 1 (25.0)
KRAS Not detected - 4 (100.0)
PIK3CA Detected NM_006218.4(PIK3CA):c.353G>A (p.Gly118Asp) 4 (100.0)
TP53 (1) Detected NM_000546.5(TP53):c.818G>A (p.Arg273His) 4 (100.0)
TP53 (2) Not detected - 4 (100.0)
TP53 (3) Detected NM_000546.5(TP53):c.742C>G (p.Arg248Gly) 4 (100.0)
TP53 (4) Not detected - 4 (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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