Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software
Table 1
Comparison of the variants detected by Sanger, by GS-Flx with SeqNext analysis, and by GS-Flx with AGSA analysis.
Gene
HGVS nomenclature
Sanger
AVA + AgsA
SeqNext
BRCA1
c.19-47del29
h
h (56%)
—
c.81-12delC
—
—
h (41%)
c.124delA
h
h (48%)
h (48%)
c.212+1G>A
h
h (72%)
—
c.342-343delTC
h
h (36%)
h (37%)
c.671-11dup
—
h (45%)
h (43%)
c.798-799del
h
h (48%)
h (48%)
c.1116G>A
h
h (43%)
h (43%)
c.1390dupA
h
h (49%)
h (48%)
c.1823-1826del
h
h (46%)
h (46%)
c.1953_1956delGAAA
h
h (35%)
h (34%)
c.2077G>A
h
h (60%)
h (62%)
c.2082C>T
H
H (100%)
H (100%)
c.2269delG
h
h (66%)
h (66%)
c.2612C>T
h
h (42%)
h (42%)
c.3113A>G
h
h (51%)
h (52%)
c.3548A>G
h
h (49%)
h (49%)
3839-3843del5ins4
h
h (52%)
h (52%)
c.4127del
h
h (56%)
h (44%)
c.4214-4215delIns5
—
—
h (23%)
c.4221delins9
—
—
h (26%)
C.4227-4237delins16
—
—
h (24%)
c.4243-4244delGA
—
—
h (26%)
c.4281_4282ins39
h
h (44%)
—
c.4308T>C
h
h (55%)
h (49%)
c.4575-4585del11
h
h (46%)
h (43%)
c.4810C>T
h
h (58%)
h (53%)
c.5266dupC
h
h (59%)
h (59%)
c.5333-20_5333-19insT
—
—
h (25%)
BRCA2
c.37_44del8
h
h (25%)
h (26%)
c.1114A>C
h
h (47%)
h (51%)
c.1246A>G
h
h (47%)
h (49%)
c.1553_1554insT
—
h (31%)
—
c.1748_1749insA
—
h (47%)
h (26%)
c.1759-1761delinsC
—
—
h (25%)
c.1774delT
—
—
h (33%)
c.1804-1806delins3
—
—
h (21%)
c.1803dupA
—
—
h (43%)
c.1815dupA
—
h (68%)
h (31%)
c.1823dupA
—
—
h (33%)
c.1833dupA
—
—
h (21%)
c.2589T>A
—
—
h (34%)
c.2803G>A
h
h (39%)
h (40%)
c.3479G>A
—
h (31%)
—
c.3807T>C
h
h (44%)
h (42%)
c.4332-4333delTA
—
—
h (66%)
c.4350dupT
—
—
h (44%)
c.4781delins3
—
—
h (22%)
c.5073dupA
h
h (42%)
h (41%)
c.5385dupA
—
—
h (22%)
c.5459_5460insA
—
h (32%)
—
c.7977-10dup
—
—
h (70%)
c.8125dupA
—
—
h (23%)
c.8147-8148insA
—
—
h (29%)
c.8574dup
—
h (38%)
h (30%)
c.8797del
—
H
—
c.8800del
—
h (80%)
—
c.8823dupA
—
—
h (28%)
c.8946dup
—
h (27%)
—
c.10083del
—
—
h (21%)
c.10115dupC
—
—
h (50%)
c.10122delC
—
—
h (32%)
False negative (out of 64)
0 (reference)
0
1
False positive (out of 64)
0 (reference)
10
28
% of reads carrying the variant is given in parentheses. Depth of the variant was <40 reads. Cells highlight false positives; cells highlight false negatives.
