rhd and rhce beadchip dna array  (Bioarray Inc)

Journal: Blood Advances

Article Title: Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia

doi: 10.1182/bloodadvances.2017007898

Figure Lengend Snippet: Comparison of allele frequencies between participants in the SWiTCH trial (n = 54) and children with SCA from CHP (n = 488)

Article Snippet: DNA samples were tested with RHD and RHCE BeadChip DNA arrays (Bioarray, Warren, NJ) and polymerase chain reaction (PCR)–based assays, as described previously.

Techniques: Comparison, Diagnostic Assay

Journal: Blood Advances

Article Title: Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia

doi: 10.1182/bloodadvances.2017007898

Figure Lengend Snippet: Mercury analysis pipeline. (A) Raw data from the sequencing instrument is passed to primary analysis software to generate sequence reads and base call confidence values (qualities). (B) Reads and qualities are passed along to a mapping tool Burrows-Wheeler algorithm (BWA) for comparison with a reference genome. The placement of reads on the reference genome produces a Binary-format Sequence Alignment Map (BAM) file and individual event BAMs were merged to make a single sample-level BAM file. (C) AtlasSNP and Genome Analysis Toolkit (GATK) are used to identify variants and produce annotated variant call files (VCFs). (D) In this study, we specifically interrogated WES data for the RHD and RHCE genes compared with conventional targeted assays.

Article Snippet: DNA samples were tested with RHD and RHCE BeadChip DNA arrays (Bioarray, Warren, NJ) and polymerase chain reaction (PCR)–based assays, as described previously.

Techniques: Sequencing, Software, Comparison, Variant Assay

Journal: Blood Advances

Article Title: Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia

doi: 10.1182/bloodadvances.2017007898

Figure Lengend Snippet: WES coverage for RHD and RHCE genes. (A) The median number of individual sequence reads are given for each polymorphism identified by exome sequencing. The sequence reads were aligned to the human reference sequence GRCh37, and median coverage was calculated for the entire SWiTCH cohort (n = 134). All exons (rectangles) had greater than 10× median coverage except RHD exon 8 (marked in red). (B) Normalized sequence read depth for RHCE exons 1, 2, and 3 (n = 54). Individuals with RHCE*Ce have a reduced ratio for exon 2 compared with exons 1 and 3 (orange bar). (C) Normalized sequence read depth for RHD, RHCE, and neighboring genes (n = 54). Genes with 2 copies are indicated as black bars, 1 copy as orange bars, and no copies as red bars.

Article Snippet: DNA samples were tested with RHD and RHCE BeadChip DNA arrays (Bioarray, Warren, NJ) and polymerase chain reaction (PCR)–based assays, as described previously.

Techniques: Sequencing

Journal: Blood Advances

Article Title: Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia

doi: 10.1182/bloodadvances.2017007898

Figure Lengend Snippet: Summary of discordance between WES and SNP methods designated by nucleotide position in cDNA and RH exon that were resolved by Sanger re-sequencing

Article Snippet: DNA samples were tested with RHD and RHCE BeadChip DNA arrays (Bioarray, Warren, NJ) and polymerase chain reaction (PCR)–based assays, as described previously.

Techniques: Sequencing

Journal: Blood Advances

Article Title: Whole-exome sequencing for RH genotyping and alloimmunization risk in children with sickle cell anemia

doi: 10.1182/bloodadvances.2017007898

Figure Lengend Snippet: Summary of RH alleles that require modification of data analysis or algorithm for assignment

Article Snippet: DNA samples were tested with RHD and RHCE BeadChip DNA arrays (Bioarray, Warren, NJ) and polymerase chain reaction (PCR)–based assays, as described previously.

Techniques: Modification, Sequencing