Application of Next-Generation–Sequencing in Hearing Loss Diagnosis - Next Generation Sequencing Technologies in Medical Genetics - page 64

Table 7.1 Perf ormance of next-generation-sequencing platforms for mutation detection of hearing loss genes
Capture-based H L gene panel PCR-based HL ge ne panel Whole exome se quencing

Target 54 known HL

genes in
human

54 known HL
genes in
human

246 known
HL genes
in human
and mouse

15 known HL
genes in
human

34 known HL
genes in
human

24 known HL
genes in
human

9 known USH
genes in
human

Human Exome Human Exome Human Exome

Target
enrichment
method

NimbleGen
solid-
based
enrichment

Agilent
SureSelect
solution-
based
enrichment

Agilent
SureSelect
solution-
based
enrichment

PCR-based
amplifi cation
enrichment

RDT
microdroplet
PCR
enrichment

RDT
microdroplet
PCR
enrichment

Long-PCR
enrichment

Agilent
SureSelect
50 Mb
enrichment

Illumina
TrueSeq
62 Mb
enrichment

Agilent
SureSelect
50 Mb
enrichment

Sequencing
platform

Roche 454 GS
FLX

Illumina GAII Illumina GAII Roche 454 GS
FLX

Illumina HiSeq
2000

Illumina HiSeq
2000

Roche 454 GS
FLX and
Illumina
GAII

Illumina
HiSeq
2000

Illumina
HiSeq
2000

SOLiD 3 or 4
Systems

Mean target
coverage

71x 903x 757x ~150x 1,585x NA NA NA NA NA

%Target
coverage
at calling
threshold

96 % 95.30 % 95 % 95 % 95 % 96 % 94 % 57 % 65 % ~50 %

Minimum
calling
threshold

3x 40x 10x 30x 30x 40x 25x 20x 20x 25x

Sensitivity 93.98 % 99.72 % NA NA 99.00 % >99.99 % NA NA NA NA

Specifi city 97.92 % >99.00 % NA NA 99.40 % >99.99 % NA NA NA NA

References Shearer et al.

( 2010 )

Shearer et al.
( 2010 )

Brownstein
et al.
( 2011 )

De Keulenaer
et al. ( 2012 )

Schrauwen et al.
( 2013 )

Sivakumaran
et al. ( 2013 )

Licastro et al.
( 2012 )

Schrauwen
et al.
( 2013 )

Schrauwen
et al.
( 2013 )

Licastro et al.
( 2012 )

HL hearing loss, RDT RainDance Technologies, NA not available