The key difference between HG19 and HG38 is that HG19 is a human reference genome that has 7 regions with alternate loci, while HG38 is a human reference genome that has 207 regions with alternate loci.
Reference genomes play an important role in mapping DNA sequences for phylogenetic and bioinformatics-based analyses. It represents a complete set of genes of an organism. In other words, it is a representation of the genome sequence of an organism. There are different reference whole genomes that are freely available to be used for genomic mapping. NCBI’s RefSeq database is one of the common sources of these kinds of reference genomes. It comprises reference genomes of different organisms, including prokaryotes, eukaryotes, and viruses. There are two main types of the reference human genomes as HG19 or GRCh37 and HG38 or GRCh38. They are human genome assemblies developed by the Genome Reference Consortium (GRC).
CONTENTS
1. Overview and Key Difference
2. What is HG19
3. What is HG38
4. Similarities – HG19 and HG38
5. HG19 vs HG38 in Tabular Form
6. Summary – HG19 vs HG38
What is HG19?
HG19, also known as the genome reference consortium human build 37 (GRCh37), is a reference genome published in 2009 by the Genome Reference Consortium. It is a haploid genome with alternate loci. There are 7 regions that depict the alternate loci in the HG19 reference genome. The HG19 reference genome was developed by sequencing the finished clones obtained from the human genome project. Furthermore, PCR products and shotgun sequences were also used in building the HG19 reference genome.
The total sequence length of the HG19 reference genome is 3,101,788,170 bps, and it consists of 249 scaffolds. Furthermore, there are 271 gaps between the scaffolds. When considering the number of clones in the component sequences, there are 27,054 clones. The reference genome comprises a total number of 24 chromosomes and plasmids.
What is HG38?
HG38, also known as the genome reference consortium human build 38 (GRCh38), is the most recent human reference genome developed by the genome reference consortium in 2017. Several loci were added to the genome, and a recent update was also released in March 2022. There are 207 regions that depict the alternate loci, which are well improved than the HG19 version. The HG38 reference genome has 349 gaps in the genome. These gaps are mostly in the regions of the telomere, centromere, and in between long repetitive sequences. PCR products and shotgun sequences are used to fill the gaps where necessary.
Figure 02: HG38
The total sequence length of the HG38 reference genome is 3,099,734,149 bps, and it consists of 473 scaffolds. When considering the number of clones in the component sequences, there are 35,614 clones. The HG38 reference genome comprises a total number of 24 chromosomes and plasmids.
What are the Similarities Between HG19 and HG38?
- HG19 and HG38 are DNA sequences.
- Both genomes are derived after the completion of the human genome project.
- Moreover, they act as reference sequences for the human genome.
- Both sequences were developed by the genome reference consortium.
- Moreover, they consist of gaps in the reference genome.
- Both HG19 and HG38 have 24 chromosomes and plasmids in their genome.
- Applications of both HG19 and HG38 are widely observed in bioinformatics and phylogenetic analyses.
What is the Difference Between HG19 and HG38?
The HG19 reference genome has 7 regions with alternate loci, while the HG38 reference genome has 207 regions with alternate loci. Thus, this is the key difference between HG19 and HG38. While the HG19 reference genome was developed in 2009, the HG38 reference genome was developed in 2017. Moreover, there are 271 gaps between scaffoldings in the HG19 genome, while the HG38 genome has 349 gaps.
The below infographic presents the differences between HG19 and HG38 in tabular form for side-by-side comparison.
Summary – HG19 vs HG38
HG19 and HG38 are human reference genomes developed by the genome reference consortium. They are important in human mapping genes in order to complete bioinformatic and phylogenetic analyses. HG19 reference genome has 7 regions with alternate loci. HG38 reference genome has 207 regions with alternate loci. The HG19 reference genome was developed in 2009, while the HG38 reference genome was developed in 2017. The number of gaps between scaffoldings of each reference genome also differs. In this regard, HG38 has more gaps showcasing advanced properties. So, this summarizes the difference between HG19 and HG38.
Reference:
1. Caetano-Anolles, Derek. “Human Genome Reference Builds – GRCH38 or hg38 – B37.” GATK.
2. Nurk, Sergey, et al. “The Complete Sequence of a Human Genome.” BioRxiv, Cold Spring Harbor Laboratory.
3. “GRCH37 – HG19 – Genome – Assembly – NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine.
4. “GRCH38 – hg38 – Genome – Assembly – NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine.
Image Courtesy:
1. “Integrated Genome Browser 9.1.0 showing chromosome 1 of the human genome assembly hg38” By Aloraine – Own work (CC BY-SA 4.0) via Commons Wikimedia