Table 1.
Targeted gene list, transcripts and design features.
Fig 1.
An outline of steps required for library preparation in the MLPA-seq.
Fig 2.
Coverage and calculated copy number ratios in the control samples (n = 8).
(A) Mean probe coverage in the control samples, normalised to compensate for library indexing differences. The error bars represent standard deviation. The horizontal line at 500x coverage represents the minimum raw probe coverage for optimal results. (B) Distribution of calculated probe ratios in the control samples. The ratio represents observed over expected copy number for each probe, with 1 equal to normal copy number. (C) Distribution of combined ratios for each targeted exon in the control samples. The vertical lines represent 0.7 to 1.3 range of ratios considered normal.
Fig 3.
Observed vs. expected copy number ratios for two mixed samples, one with BRCA1 exon 12 duplication and another with BRCA1 exons 1–23 deletion.
The error bars represent standard deviation of probe ratios.
Table 2.
Analytical sensitivity for detection of somatic amplifications of CCNE1 and ERBB2 genes in tumour samples—concordance between ISH assay and results from the MLPA-seq.
Table 3.
Analytical sensitivity for detection of germline copy number changes in BRCA1 and BRCA2 genes in normal, tumour and ascites samples—concordance between MLPA and results from the MLPA-seq.
Fig 4.
Ratios for BRCA1, BRCA2 genes for three reproducibility samples, prepared by three operators.
The red line indicates the lower limit of normal ratio variation (0.7), the blue line the upper limit of normal ratio variation coverage (1.3).