Fig. 2

Genomic annotation of the TRB gene cluster on chromosome 7q34. a Annotated UCSC genes in NCBI36/hg18 (genome-euro.ucsc.edu); b Sequence alignments of genome freezes NCBI36/hg18 and GRCh37/hg19 with chromosomal positions, similar or identical sequences (grey and black bars, respectively), unique/ unaligned sequences (white), sequences identified to be inverted in freeze hg19 are given below the baseline; c PCR products specific for inversion GRCh37/hg19 (arrows); d-i Magnification (dotted box/ lines) of genome freeze NCBI36/hg18; d Genomic position of frequent TRB deletion, chromosomal position and UCSC genes; e Positions of array-markers: upper row = SNP markers; lower row = CN markers; solid black line = most common, minimal size of deletion (13,136 bp or 28 markers). The dashed line indicates one additional array-marker that is commonly deleted as well (deletion of 16,338 bp or 29 markers); f Positions of pairs of MLPA probes (asterisks) encompassing the TRB locus. Probes marked in purple encompass the CNV, probes marked in red are located within the deletion (see Fig. 1a-c); g Arrows indicate PCR primers for amplicons specific to NCBI36/hg18 (arrows); h Segmental duplication of 90–98% similarity (grey patterned bars); i Homologous sequences in the first and second part of the segmental duplication (indicated by bar of same color)