Table 2.

Summary of results from phase 2 of the study, in which PCR primers and conditions were controlled.^a^,^b

Variant	Transcripts	Phase 2 results (10 sites)^c
Variant	Transcripts	1^*	2^{^}	3^*	4^*	8^{^}	9^{^}	16^*	17^*	18^*	19^*
Unequivocal
BRCA2 c.9501+3A>T	Full length	+	+	+	+	+	+	+	+	+	+
	Δ25^d	+	+	+	+	+	+	+	+	+	+
	ins i23^d	-	+	-	-	-	-	-	-	-	-
BRCA2 c.8632+1G>A	Full length	+	+	+	+	+	+	NA	+	+	+
	Δ19^d	-	-	-	-	+	-		-	-	-
	Δ20^d	+	+	+	+	+	+		+	+	+
	Δ19&20^d	+	+	-	-	+	+		+	-	-
	ins i20^d	-	+	-	+	-	-		-	-	-
	Extra peaks^d	-	+	-	-	-	-		-	-	-
BRCA1 c.135-1G>T	Full length	+	+	+	+	+	+	NA	+	+	+
	Δ5q^d	+	+	-	-	+	-		+	-	-
	Δ5^d	+	+	+	+	+	+		+	+	+
	Δ3^d	-	+	-	-	+	-		-	-	-
	Δ3,5^d	-	+	-	-	+	-		-	-	-
	Δ5,6^d	-	+	-	-	-	-		-	-	-
	ins i3^d	-	+	-	-	+	-		-	-	-
	ins i3+Δ5^d	-	+	-	-	-	-		-	-	-
BRCA1 c.5467+5G>C	Full length	+	+	+	+	+	+	+	+	+	+
	Δ21^d	-	-	-	-	+	-	-	-	-	-
	Δ21,23^d	-	-	-	-	+	-	-	-	-	-
	Δ22,23^d	-	+	-	-	+	-	-	+	-	-
	Δ23^d	+	+	+	+	+	+	+	+	+	+
	Δ22^d	-	+	-	+	+	-	-	-	-	-
Equivocal
BRCA2 c.7988A>T	Full length	+	+	+	+	+	+	+	+	+	+
	Δ18	+	+	+	+	+	+	+	+	+	+
	Δ17&18	+	+	+	+	+	+	+	+	+	+
BRCA2 c.426-12_8delGTTTT^*	FL	+	+	+	+	+	+	NA	+	+	+
	Δ6q,7	+	+	-	+	+	-		+	-	-
	ins 18bp^d	-	-	-	-	-	+		-	-	-
	Δ5^d	+	+	+	+	+	+		+	+	+
	Δ5,6,7^d	-	+	-	-	+	-		+	-	-
	Δ6,7^d	-	-	-	-	-	+		-	-	+
BRCA1 c.591C>T	Full length	+	+	+	+	+	+	+	+	+	NA
	Δ9	-	+	+	+	+	-	+	+	-
	Δ9,10	+	+	+	+	+	+	+	+	+
	Δ9,10,11q	+	+	+	-	+	+	+	+	-
	Δ9,10,11	-	+	-	+	+	-	-	-	-
	Δ11q	+	+	+	-	+	+	+	+	-
	Δ9,11q^d	+	+	-	-	+	-	+	-	-
	Δ10,11q^d	-	-	-	-	+	-	-	-	-
	Δ10	-	+	-	-	+	-	-	-	-
	Δ11q+insi13^d	-	+	-	-	+	-	-	-	-
	ins i21 intron 9^d	-	-	-	-	+	-	-	-	-
	Extra peaks^d	-	+	-	-	-	-	-	-	-
BRCA1 c.594-2A>C	Full length	+	+	+	+	+	+	+	+	+	NA
	Δ9	-	+	-	-	+	+	-	-	-
	Δ9,10	+	+	+	+	+	+	+	+	+
	Δ9,10,11q	+	+	+	-	+	+	+	+	-
	Δ9,10,11	+	+	-	-	-	+	-	-	-
	Δ10^d	+	+	+	+	+	+	+	+	+
	Δ11q	+	+	+	+	+	+	+	+	-
	ins i21^d	-	+	-	-	+	-	-	-	-
	Δ9,11q^d	-	+	-	-	+	+	+	-	-
	Δ10,11q^d	-	+	+	-	+	+	+	+	-
	Δ11q+insi13^d	-	+	-	-	+	-	-	-	-
		*Phase 2 BRCA1* c.67-2A>G results (12 sites)**^c
		1^*	2^{^}	3^*	4^*	8^{^}	9^{^}	16^*	17^*	18^*	20^{^}	21^*	22^{^}
BRCA1 c.671-2A>G	Full length	+	+	+	+	+	+	+	+	+	+	+	+
	Δ9	-	+	+	-	+	-	-	-	-	+	-	-
	Δ9,10	+	+	+	+	+	+	+	+	+	+	+	-
	Δ9,10,11	+	+	+	+	+	+	+	+	-	+	+	-
	Δ9,10,11q	+	+	-	-	+	+	-	-	+	-	-	-
	Δ10^d	-	+	-	-	+	-	-	-	-	-	-	-
	Δ11	+	+	+	+	-	+	+	+	+	+	-	+
	Δ11q	-	+	-	+	+	+	-	-	+	+	-	+
	Δ9,10,11,12^d	-	-	-	-	-	-	+	-	-	-	-	-
	Δ9,11^d	-	+	-	-	-	-	-	-	-	-	-	-
	Δ10,11^d	+	+	+	+	+	+	+	+	-	-	-	+
	Δ10,11q^d	-	-	-	-	+	-	-	-	-	-	-	-
	Δ11&12^d	-	+	-	-	-	-	-	-	-	+	-	-
	Δ∼3.2kb exon 11^d	+	-	-	-	-	-	-	-	-	-	-	+
	Δ9,11q^d	-	+	-	-	+	-	-	-	-	-	-	-
	ins i21^d	-	-	-	-	+	-	+	-	-	-	-	-
	Δ11q+insi13^d	-	+	-	-	+	-	-	-	-	-	-	-

+, Detection of the transcript; –, no detection.

Transcripts were identified in at least one control. The Δ6,7 transcript identified in the analysis of BRCA2:c.426-12_8delGTTTT is not sequence confirmed and it is possible that this transcript is actually Δ6q,7, which differs by only 2 bp. Splice slipping events were also reported by several sites, for example 442_444del3 from BRCA1c.591C>T by site 11. Δ8pand Δ14p splice slipping events were also reported by site 11 and 17 following a review of the data after results were initially compiled. Additional minor and uncharacterized peaks were detected by some sites but have not been included in the table. HGVS (Human Genome Variation Society) nomenclature descriptions are available in online Supplemental Table 3.

Agarose gel detection;

^{^}

other detection; NA, not assessed. Sites 2 and 8 used capillary EP, 9 used Qiaxcel, 20 used MultiNA, 22 used Labchip GX.

Transcripts detected in the variant carrier only. Other transcripts were identified in at least 1 control.