hg19 (grch37) vs. hg38 (grch38) human genome reference comparison zuotian tatum department of human...
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hg19 (GRCh37) vs. hg38 (GRCh38)
Human Genome Reference Comparison
Zuotian Tatum
Department of Human Genetics
Leiden University Medical Center
Timeline 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.nih.gov/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
Non-nuclear genome: Yes
http://www.ncbi.nlm.nih.gov/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 available (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 false 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 Collaboration (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 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 assembly unit.
Unlocalized scaffolds from the GRCh38 Primary Assembly unit.
Unplaced scaffolds from the GRCh38 Primary Assembly unit.
Epstein-Barr virus (EBV) sequence Note: 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 often 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 units
RNASeq quantification - Fragments (reads) per million per killobase (FPKM/RPKM) values to quantify gene expression
- Unique mapping only Analysis tools do not distinguish allelic duplication from paralogous duplication
- Non overlapping gene regions
To understand the effect of alt-loci on RNASeq quantification Compare alignment of chromosome 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 RNASeq
hg19 hg38
mapped 14,655,299 14,704,427
mappedDiffChr 4,959 4,017
mappedPairProper 14,639,261 14,690,090
mappedPairProperPct 92.62 92.94
total 15,805,561 15,805,561
totalSplice 5,060,829 5,078,133
unmapped 1,150,262 1,101,134
hg19: with alt locihg38: without alt loci
HLA-A hg19 full set – chr6
D1
hg19 full set – chr6_mann_hap4
D1
hg19 full set – chr6_qb1_hap6
D1
hg19 full set – chr6_dbb_hap3
D1
MHC 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 function
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
duplication
A graph structure is a natural way to represent a population-based genome assembly
Conclusions RPKM values are highly correlated between hg19 and hg38.
Analysis set is preferred for expression analysis. Additional analysis may be performed to use the
alt-loci separately.
Annotations for hg38 is still lacking and need contribution from the community.
Improve modeling of genome variability in population.