(完整版)hg19(GRCh37)与hg38(GRCh38)数据差异比较

1、hg19 (grch37) vs. hg38 (grch38)human genome reference comparisonzuotian tatumdepartment of human geneticsleiden university medical centertimeline grch37: first release: feb 27, 2009 latest patch: jun 28, 2013 (p13) grch38: first release: dec 24, 2013 latest patch: oct 14, 2014 (p1)http:/www.ncbi.nlm

2、./projects/genome/assembly/grc/human/data/content grch37.p13: total bases: 3.23 billion 2.99 billion (without n) n50: 46 million number of alternative loci: 9 non-nuclear genome: no grch38.p2: total bases: 3.21 billion 3.05 billion (without n) n50: 67 million number of alternative loci : 261

3、non-nuclear genome: yes/projects/genome/assembly/grc/human/data/ucsc tracks for grch38 ucsc refseq available since april 2014. ensembl regulatory build available since september 2014. dbsnp 141 available since october 2014. encode and fantom5 track hubs are still not availa

4、ble (nov 2014).new in grch38 release three new sequence files, in addition to the standard assembly files: - gca_000001405.15_grch38_top-level.fna.gz - gca_000001405.15_grch38_no_alt_analysis_set.fna.gz - gca_000001405.15_grch38_full_analysis_set.fna.gz the analysis set files are created to avoid fa

5、lse mapping in ngs alignment pipelines.gca_000001405.15_grch38_top-level.fna.gz all the top-level objects in the full-assembly chromosomes unlocalized scaffolds unplaced scaffolds alternate locus scaffolds mitochondrial genome the sequence identifiers are international sequence database collaboratio

6、n (insdc) accession.versions and the definition lines are genbank style. no sequences have been hard-masked.gca_000001405.15_grch38_no_alt_analysis_set.fna.gz chromosomes from the grch38 primary assembly unit.note: the two par regions on chry have been hard-masked with ns. the chromosome y sequence

7、provided therefore has the same coordinates as the genbank sequence but it is not identical to the genbank sequence. similarly, duplicate copies of centromeric arrays and wgs on chromosomes 5, 14, 19, 21 & 22 have been hard-masked with ns. mitochondrial genome from the grch38 non-nuclear assembl

8、y unit. unlocalized scaffolds from the grch38 primary assembly unit. unplaced scaffolds from the grch38 primary assembly unit. epstein-barr virus (ebv) sequencenote: the ebv sequence is not part of the genome assembly but is included in the analysis set as a sink for alignment of reads that are ofte

9、n present in sequencing samples.gca_000001405.15_grch38_full_analysis_set.fna.gz = gca_000001405.15_grch38_no_alt_analysis_set.fna.gz + alt-scaffolds from the grch38 alt_ref_loci_* assembly unitsalt-loci add complexity to rnaseq quantificationideogram of grch38.p2rnaseq quantification- fragments (re

10、ads) per million per killobase (fpkm/rpkm) values to quantify gene expression- unique mapping onlyanalysis tools do not distinguish allelic duplication from paralogous duplication- non overlapping gene regionsto understand the effect of alt-loci on rnaseq quantification compare alignment of chromoso

11、me 6 mhc region between - hg19 full set with 7 alt-loci - hg38 analysis set without alt-loci sequence content are largely unchanged between hg19 and hg38.mapping/alignment for rnaseqhg19hg38mapped14,655,29914,704,427mappeddiffchr4,9594,017mappedpairproper14,639,26114,690,090mappedpairproperpct92.629

12、2.94total15,805,56115,805,561totalsplice5,060,8295,078,133unmapped1,150,2621,101,134hg19: with alt locihg38: without alt locieffect of alt loci in rnaseq alignments0.010.11101001000100000.010.1110100100010000gene rpkm (hg19)gene rpkm (hg19)c chr_m askedhr_m asked171946xgene rpkm (hg38)distribution o

13、f rpkm differencemajor histocompatibility complex region on chromosome 6hla-ahg19 full set chr6d1hg19 full set chr6_mann_hap4d1hg19 full set chr6_qb1_hap6d1hg19 full set chr6_dbb_hap3d1hla-ahg19 full set chr6hg38 analysis setd1d2d3d1d2d3hla-chg19 full setd1d2d3hg38 analysis setd1d2d3hla-drahg19 full

14、 setd1d2d3hg38 analysis setd1d2d3major histocompatibility complex region on chromosome 6class iiimhc class iii 700kb stretch, 60 genes. the most gene-dense region of the human genome 14% coding 72% transcribed highly conserved only a free have clearly defined and proven functiontnfhg19 full set chr6

15、d1.controld1.treatedhg38 analysis set chr6d1.controld1.treatedhighly variant immune regions retiledlilra3 moved to alt-loci in hg38hg19hg38lilrb2lilra3lilra5 lilrb2 lilra5phantom lilra3lilra3 in hg19intergeniclilrb3lilra4lilrb5gene length calculation we need gene length for calculating rpkm. if alig

16、nment uses alt loci rpkm would be artificially lowered for alt loci genes. if alignment does not alt loci remove alt loci annotations from the official set.need more comprehensive approach to genome variation.assembly model is neither haploid nor diploid analysis tools penalize reads mapping to 1 location do not distinguish allelic duplication from paralogous duplicationa graph structure is a natural way to represent a population-based genome assemblyconclusions rpkm values are highly correlated between hg19 and hg38. analysis set is preferre