PMC

Pairwise F_st of Copy-Number Variant Loci in Nine Human Populations
Heatmaps representing pairwise F_st values between populations calculated based on CNV allele frequency data generated at four loci are as follows: (A) IGHV7-4-1 insertion; (B) IGHV3-9, IGHV1-8, IGHV5-a, and IGHV3-64D complex event; (C) IGHV1-c, IGHV3-d, IGHV3-43D, and IGHV4-b insertion; and (D) IGHV1-69D, IGHV1-f, IGHV3-h, and IGHV2-70D insertion. Population abbreviations are shown on both map axes. Colors in each square correspond to a given F_st value range as indicated by the key.

Schematic Comparisons of IGHV Haplotype between CH17 and the Human Reference Genome Assembly (GRCh37)
(A) Functional and ORF IGHV genes annotated from each reference are depicted by filled boxes with corresponding IGHV gene locus and allele identifiers located above and below the haplotypes.
(B) The positions of two insertions and two complex events characterized from the CH17 haplotype are shown mapped to the GRCh37 IGH human reference assembly sequence (black line; chr14:105,928,955-107,289,540). The locus is presented in the same orientation as that depicted by IMGT. Functional and ORF IGHV, IGHD, and IGHJ genes (not to scale) and IGHV pseudogenes are shown (to scale); the names of IGHV genes involved in the characterized structural variants are indicated. Segmental duplications downloaded from the UCSC genome browser are shown below GRCh37.

Map of IGHV CNVs Identified by Complete Sequencing of Fosmid Clones
The positions of three deletions, two insertions, one duplication, and one complex event characterized from fosmid alternative haplotypes are shown mapped to the GRCh37 IGH reference (black line; chr14:105,928,955–107,289,540) with the same parameters as in B. The locus is presented in the same orientation as that depicted by IMGT. Functional and ORF IGHV, IGHD, and IGHJ genes (not to scale) as well as IGHV pseudogenes are shown (to scale); the names of IGHV genes involved in the characterized structural variants are indicated. Segmental duplications downloaded from the UCSC genome browser are shown below GRCh37. The large red box indicates a hotspot region of recurrent mutation (see for additional haplotypes associated with this hotspot). The deletion of IGHV4-61 was identified by Mills et al. (chr14:107,084,861–107,096,738) and was also included in our analyses.

A Hotspot of IGH Structural Polymorphism
Each of the five identified haplotypes harboring diverse CNVs is shown relative to GRCh37. Each haplotype is labeled with a sample identifier, and the length (kbp) is indicated at the right of each haplotype in parentheses. Two haplotypes in this region were identified from the individual NA18555 (haplotypes A and B). One to four ∼25 kbp segmental duplication sequence blocks (or partial blocks), depending on the haplotype, are depicted by shaded blue bars. Deleted regions identified in five of the haplotypes, including GRCh37, are indicated by red dotted lines. The positions and names of functional IGHV genes (green boxes) are shown in each haplotype. The partial haplotype identified in this region from individual NA19240 (AC234301), which overlapped that of NA18555 haplotype A and included the genes IGHV4-30-2, IGHV3-30-3, IGHV4-30-4, and IGHV3-30-5, is not depicted but was included in the analysis and allowed for the placement of the NA18502 haplotype (also see and ).

Breakpoint Analysis of the IGHV3-23 Duplication
(A) Pairwise BLAST alignment of 38 kbp region surrounding IGHV3-23 in GRCh37 (chr14:106700594–106738594). Brown and orange dotted arrows point to ∼5.3 kbp repeat sequences (extended homology) suspected to have mediated the IGHV3-23 duplication. Repeat sequences show 86% sequence identity.
(B) Sequence harboring the IGHV3-23 duplication identified in individual NA18956 (clones AC244473 and AC206018) is compared to GRCh37 (chr14:106700594–106738594). Regions of similarity between the two haplotypes are connected by black lines. Segments colored in blue in both haplotypes indicate the locations of the 10.8 kbp duplicates. Brown and orange bars above the NA18956 haplotype and below the GRCh37 haplotype indicate ∼5.3 kbp repeat sequences identified by BLAST in (A). Labeled IGHV genes and pseudogenes are depicted by green and red chevrons, respectively.
(C) A five-way alignment of ∼5.3 kbp repeat sequences from both haplotypes. Alignment of base positions is shown along the top of the diagram. Each repeat sequence (three from NA18956 and two from GRCh37) is represented by a single horizontal black line. Blue tick marks on each line indicate nucleotide (nt) differences and gaps observed between the aligned sequences. The red line tracks the most similar alignment of the middle NA18956 repeat sequence to the other four sequences. Based on nt similarity, the event breakpoint is presumed to have occurred within the 373 bp region (red box) in which all aligned sequences share 99.7% sequence identity (372/373 nt).