Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome

Abstract

BackgroundAlthough the reference human genome sequence was declared finished in 2003, some regions of the genome remain incomplete due to their complex architecture. One such region, 1q21.1-q21.2, is of increasing interest due to its relevance to human disease and evolution. Elucidation of the exact variants behind these associations has been hampered by the repetitive nature of the region and its incomplete assembly. This region also contains 238 of the 270 human DUF1220 protein domains, which are implicated in human brain evolution and neurodevelopment. Additionally, examinations of this protein domain have been challenging due to the incomplete 1q21 build. To address these problems, a single-haplotype hydatidiform mole BAC library (CHORI-17) was used to produce the first complete sequence of the 1q21.1-q21.2 region.ResultsWe found and addressed several inaccuracies in the GRCh37sequence of the 1q21 region on large and small scales, including genomic rearrangements and inversions, and incorrect gene copy number estimates and assemblies. The DUF1220-encoding NBPF genes required the most corrections, with 3 genes removed, 2 genes reassigned to the 1p11.2 region, 8 genes requiring assembly corrections for DUF1220 domains (~91 DUF1220 domains were misassigned), and multiple instances of nucleotide changes that reassigned the domain to a different DUF1220 subtype. These corrections resulted in an overall increase in DUF1220 copy number, yielding a haploid total of 289 copies. Approximately 20 of these new DUF1220 copies were the result of a segmental duplication from 1q21.2 to 1p11.2 that included two NBPF genes. Interestingly, this duplication may have been the catalyst for the evolutionarily important human lineage-specific chromosome 1 pericentric inversion.ConclusionsThrough the hydatidiform mole genome sequencing effort, the 1q21.1-q21.2 region is complete and misassemblies involving inter- and intra-region duplications have been resolved. The availability of this single haploid sequence path will aid in the investigation of many genetic diseases linked to 1q21, including several associated with DUF1220 copy number variations. Finally, the corrected sequence identified a recent segmental duplication that added 20 additional DUF1220 copies to the human genome, and may have facilitated the chromosome 1 pericentric inversion that is among the most notable human-specific genomic landmarks.

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

“…In the present contribution, we use a genome mapping system 1,2,23 to make massively parallel measurements of DNA extension at the single-molecule level on barcoded DNA molecules. The approach begins with sheared, labeled genomic DNA from E. coli.…”

An Incomplete Understanding of Human Genetic Variation

“…mCNV breakpoints frequently are flanked by high-identity repetitive sequence, further limiting imputation and association of this form of genetic variation with human phenotypes. Haplotyperesolved sequencing of these regions has consistently shown that such inferential genotyping underestimates the genetic complexity of the underlying genetic variation of these regions (Boettger et al 2012;Steinberg et al 2012;Antonacci et al 2014;O'Bleness et al 2014). Several lines of evidence suggest that this missing variation will be critical to interpreting the "missing heritability" of human disease.…”

Phylogenetic analysis supports a link between DUF1220 domain number and primate brain expansion

“…In primates, this ancestral domain has been duplicated many times over, reaching its peak abundance in humans where several hundred DUF1220 domains exist across 20-30 genes in the Nuclear Blastoma Breakpoint Family (NBPF) (Vandepoele et al 2005;Dumas et al 2012). The majority of these map to 1q21.1, a chromosomal region with complex, and unstable genomic architecture (O'Bleness et al 2012(O'Bleness et al , 2014.…”