Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis

Table 1 Cohort of patients diagnosed with Duchenne muscular dystrophy (DMD)

Sample ID	Identifier	Detection method	SV identified	SV size (bp) by NGM	Coverage by NGM
CDMD1003	Proband	PCR	Hemizygous deletion (exons 46–51)	–182,665	72x
CDMD1155	Proband	MLPA	Hemizygous deletion (exons 48–54)	–224,364	104x
CDMD1156	Proband	MLPA	Hemizygous deletion (exons 49–50)	–59,771	74x
CDMD1159	Proband	MLPA	Hemizygous deletion (exon 52)	–45,839	90x
CDMD1131	Proband	PCR, MLPA	Hemizygous deletion (exons 45–partial 51)	–250,092	118x
CDMD1132	Mother	aCGH	Heterozygous deletion (exons 45–51 [carrier])	–249,994	96x
CDMD1157	Proband	MLPA	Hemizygous deletion (exons 46–51)	–184,882	85x
CDMD1158	Mother	N/A	Unknown before NGM; Not a carrier of exons 46–51 deletion	N/A	80x
CDMD1163	Proband	aCGH	Hemizygous duplication (exons 3–4)	+12,968	87x
CDMD1164	Mother	N/A	Unknown before NGM; carrier of exons 3–4 duplication	+12,857	158x
CDMD1187	Proband	PCR, MLPA, RNA-seq, WGS	Hemizygous inversion (exons 38–end)	5.1 Mb	90x

Cases with SV in DMD are shown. The “detection method” column describes methods used to identify affected exons of DMD. The “+” and “-” signs in the “SV size (bp) by NGM” column represent gain or loss of DNA material, respectively. The last column describes the effective genome coverage (defined as the total amount of the data produced in base pairs divided by the genome size [3.2 Gbp in the case of humans] and multiplied by molecule-to-reference map rate (typical range 55–85%).
PCR polymerase chain reaction, RNA-seq RNA sequencing, WGS whole-genome sequencing, MLPA multiplex ligation-dependent probe amplification, aCGH microarray-based comparative genomic hybridization

ISSN: 1756-994X