Additional file 3.

Table S1. Overview of Sample Processing: RainDance Sequence Enrichment, SOLiD Sequencing Library Construction and Sample Indexing, Emulsion PCR and Sequencing. The samples were enriched on the RDT1000, followed by shearing and standard library construction according to the SOLiD 3.0 protocol (Applied Biosystems/ Life Technologies, USA). Six individual libraries were prepared using the enriched gDNA products and indexed with barcodes 1 to 6 (Library IDs 759L, 760L, 761L, 762L, 763L and 764L). Three additional libraries were prepared using the enriched WGA products and indexed with barcodes 9 to 11 (Library IDs 765L, 766L and 767L). To test the performance of each step, the non-amplified samples were pooled before and after the library preparation process. Pre-library preparation pools were created by combining an equimolar portion of the 6 individual gDNA. The samples were pooled together and processed as single samples (Library IDs 768_1L and 768_2L were duplicate libraries that contained six gDNA samples). Post-library preparation pools were created by combining equimolar portions of each individual sample post library preparation. A post library preparation pool was generated before emPCR (Emulsion ID 770em: gDNA samples 1, 2, 3, 4 and 6) and after emPCR (Emulsion ID 792em: gDNA samples 1, 2, 3, 4, 5 and 6). The resulting PCR products were sequenced on a SOLiD 3.0 system using 50 bp fragment libraries. Table S3. CLC Bio SNP Detection Parameters. The following parameters were used for SNP detection through the CLC bio Genomics Workbench (version 3.0): Maximum coverage 50000. Maximum gap and mismatch count 2. Minimum average quality 15. Minimum central quality 20. Minimum coverage 5. Minimum variant frequency (%) 10.0. Variant count threshold 50000. Window length 11. In the non-pooled samples, a SNP with a non-reference allele frequency of 10-90% was considered a heterozygote. A homozygous SNP in non-pooled samples was defined as having >90% non-reference allele frequency. Table S4. Coverage Metrics CLC bio Genomics Workbench (version 5.1). Table S6. Sequence Data Generated Using 454 FLX and Illumina of the same Target Regions (172kb/384 exons). Table S7. Sample Multiplexing Calculation for the RDT 384 Member Panel and SOLiD Sequencing Platform.

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ElSharawy et al. BMC Genomics 2012 13:500   doi:10.1186/1471-2164-13-500