Human Genome Overview

Information concerning continuing improvement of the human genome.

The most recent assembly for human is GRCh37 (download the assembly). This is the first assembly produced by the GRC and is considered the next version of NCBI Build 36 (also known as hg18). Improvements in this assembly include:

• Closure of 25 unspanned gaps found in Build 36
• Resolution of over 150 issues reported as problems in Build 36
• Addition of alternate loci for three complex regions, including the MHC region.
• Standardization of AGPs, including the addition of biological gap information.

GRCh37 is a haploid assembly,constructed from multiple individuals and can be divided into a 'primary assembly' and a set of 'alternate loci'. The primary assembly represents the assembled chromosomes, plus any unlocalized or unplaced sequence that represent the non-redundant, haploid assembly.The alternate loci represent regions for which there is large scale variation and an alternate tilng path is available for this region. An example of such a region can be found at chromosome 17q21.31, often known as the MAPT locus. This region was described as carrying an inversion polymorphism (PMID: 15654335) and has been associated with various phenotypes (PMID: 16718704; PMID: 18628315). The version of this region in Build 36 was actually a mosaic of both haplotypes (as tracked in HG-77) and has been resolved in GRCh37 thanks to data described in Zody et al., 2008 (PMID: 19165922).

Information on alternate loci

Chromosome region with alternate loci	Length of region	Number of alternate contigs in region	View Region
UGT2B17 region (chr4:69,170,077-69,877,175)	707,099 bp	1 contig	view
contig name contig acc contig length contig span View Region HSCHR4_1_CTG9 GL000257.1 590,426 chr4:69,170,077-69,878,175 view
MHC region (chr6: 28,477,797-33,448,354)	4,970,558 bp	7 contigs	view
contig name contig acc contig length contig span View Region HSCHR6_MHC_APD_CTG1 GL000250.1 4,622,290 chr6: 28,696,604-33,335,493 view HSCHR6_MHC_COX_CTG1 GL000251.1 4,795,371 chr6: 28,477,797-33,351,542 view HSCHR6_MHC_DBB_CTG1 GL000252.1 4,610,396 chr6: 28,696,604-33,225,977 view HSCHR6_MHC_MANN_CTG1 GL000253.1 4,683,263 chr6: 28,696,604-33,225,977 view HSCHR6_MHC_MCF_CTG1 GL000254.1 4,833,398 chr6: 28,696,604-33,359,642 view HSCHR6_MHC_QBL_CTG1 GL000255.1 4,611,984 chr6: 28,696,604-33,379,750 view HSCHR6_MHC_SSTO_CTG1 GL000256.1 4,928,567 chr6: 28,659,143-33,448,354 view
MAPT region (chr17: 43,384,864-44,913,631)	1,528,768 bp	1 contig	view
contig name contig acc contig length contig span View Region HSCHR17_1_CTG5 GL000258.1 1,680,828 chr17: 43,384,864-44,913,864 view

References relevant to the genome assembly

• Adaptive evolution of UGT2B17 copy-number variation (Xue et al., 2008)
• Evolutionary toggling of MAPT 17q21.31 inversion region (Zody et al., 2008)
• Closing gaps in the human genome using sequencing by synthesis (Garber et al., 2009)