Genome Update: Representing variation in the LRC on chr. 19q13.4

Human GRCh37 patch release 5 includes eight NOVEL patches representing different haplotypes in  the Leukocyte Receptor Complex (LRC) region on chromosome 19q13.4 (GL949746.1, GL949747.1, GL949748.1, GL949749.1, GL949750.1, GL949751.1, GL949752.1, GL949753.1). This region contains multiple clusters of genes belonging to the immunoglobulin superfamily, including killer immunoglobulin-like receptors (KIRs), leukocyte immunoglobulin-like receptors (LILRs) and leucocyte-associated immunoglobulin-like receptors (LAIRs). The LRC complex is of major importance in human disease across a wide context. Research efforts have focused in particular on the KIR cluster, since this ~150kb  region displays extensive haplotypic variation due to both differences in coding sequences and the presence or absence of particular loci. Several reports indicated problems with the representation of the LRC region in both NCBI36 and GRCh37. In GRCh37, one improvement was made when the NCBI36 chr. 19 unlocalized scaffold NT_113949.1, which contained a second representation of this region, was determined to be mis-assembled and was excluded from the assembly (tracked in HG-196). However, in both assembly versions, the chromosome 19 sequence for this variable region is derived from multiple clone libraries, suggesting a haplotype representation problem. On-going GRC efforts to replace this region of chromosome 19 in future assembly versions with a new single haplotype  from the CHOR...
Source: GenomeRef - Category: Genetics & Stem Cells Source Type: blogs