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Genomic technologies
Published in Wendy A. Rogers, Jackie Leach Scully, Stacy M. Carter, Vikki A. Entwistle, Catherine Mills, The Routledge Handbook of Feminist Bioethics, 2022
The Human Genome Project (HGP), an international consortium effort to map the entire human genome, has not produced the complete transformation in therapeutic medicine that was predicted (Collins 1999). But with the publication of the human reference genome in 2003, the HGP did usher in the genomic era (Collins et al. 2003). Indeed, in spite of falling short of the hype regarding the clinical promises, the HGP has had a substantial impact on the biomedical sciences by fueling technological advances involving high-throughput sequencing, high-resolution data and large-scale bioinformatics. Almost every field in biological research and clinical practice has been influenced by the introduction of genomic technologies.
Genetics and exercise: an introduction
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Claude Bouchard, Henning Wackerhage
Improved DNA sequencing methods have allowed researchers to sequence thousands of whole human genomes, and this has informed us about how much genetic variability there is compared to the standard human reference genome. Whilst the sequencing of the first human genome took about 20 years, at a cost of $3 billion, today a human genome can be sequenced in a day for less than $1,000, thanks to the development of next generation DNA sequencing methods (33). These next generation sequencing methods were used to sequence the genome of James Watson (34) followed by the genomes of many others. Collectively, these sequencing experiments have shown that the typical human genome carries about 4–5 million DNA variants not found in the human reference sequence. About 20 million of the 3.6 billion base pairs, or 0.6% of the DNA sequence of an individual genome, differ when compared to the human reference genome (24). More than 99% of these DNA variants are SNPs and short INDELs. Additionally, a typical human genome has up to 2,500 structural or chromosomal variants which include about 1,000 large deletions and 160 copy number variants. Finally, an individual selected at random also carries from 200,000 up to 500,000 rare variants that have arisen in recent times.
The Evolution of Anticancer Therapies
Published in David E. Thurston, Ilona Pysz, Chemistry and Pharmacology of Anticancer Drugs, 2021
The original goal of the HGP was to map the nucleotides contained in a human haploid reference genome (i.e., more than three billion base pairs). As the genome of any given individual is unique, the HGP involved the sequencing of a small number of individuals and then combining the data to get a complete sequence for each chromosome. Therefore, the finished human genome was a composite, not representing any one particular individual.
Lost in translation: the pitfalls of Ensembl gene annotations between human genome assemblies and their impact on diagnostics
Published in Expert Review of Molecular Diagnostics, 2023
Mohammed O. E. Abdallah, Mahmoud Koko, Raj Ramesar
The human reference genome has been continually updated since the release of the first draft human genome. Whereas a telomere-to-telomere assembly (T2T) released in 2022 is the most complete and only gap-free human genome assembly so far, the current default assembly for Ensembl is GRCh38 (also known as hg38), released in 2013 [1]. Despite all its imperfections, the previous human genome assembly GRCh37 (also known as hg19) which was released in 2009 is still the predominant human genome assembly in current use. An obvious explanation for this lag in adopting the newest assembly is the availability of vast amounts of relational genomic annotations for the previous assembly (GRCh37) that are not yet ported to the current ones, as well as the incurred cost of remapping or recalling genomics data under the new assembly. We previously raised the issue of minor reference alleles in the GRCh37 assembly, how it adversely impacts variant calling, and its implications especially for recessive genetic disorders [2]. In this correspondence, we highlight another pressing issue that is related to GRCh37 annotations.
Genomic diversity of Helicobacter pylori populations from different regions of the human stomach
Published in Gut Microbes, 2022
Daniel James Wilkinson, Benjamin Dickins, Karen Robinson, Jody Anne Winter
Curated reads were used to construct de novo assemblies using the SPAdes68 3.11.1 assembler in careful mode creating consensus whole-genome assemblies for the deep-sequenced clinical sweep samples and contigs <500 bp were removed. For analysis of strains from multiple regions of the same stomach (Fig. 1C; Suppl. Figure 5C, 7C, 9C, 10C, 11C, 12C, 13C, 14C, 15, 16), a patient-specific combined antrum and corpus consensus assembly was de novo assembled using the same settings by combining the curated reads from both antrum and corpus regions. This was done to reduce the reference bias associated with using either the consensus assembly from the deep sequenced antrum or corpus populations. For strains isolated from patients where only one region was population deep sequenced, the population consensus assembled genome sequence from that region was used as the reference genome. Sequencing depth/coverage was determined using mosdepth 0.2.3.69 Contaminant reads were assembled into separate contigs and excluded from all further analyses with the exception of BLAST ring image generator (BRIG; version 0.95) analysis19 in Suppl. Fig 8–9.
Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome
Published in Gut Microbes, 2022
Hao Jin, Lijun You, Feiyan Zhao, Shenghui Li, Teng Ma, Lai-Yu Kwok, Haiyan Xu, Zhihong Sun
KneadData v0.7.5 (http://huttenhower.sph.harvard.edu/kneaddata) was used to remove the low-quality and human genome sequences for short-read sequencing data. The long reads were mapped to the human reference genome (GRCh38) using minimap246 (“-x asm5”) to remove human genome sequences. An integrated hybrid metagenomic assembly methodology was employed to construct “super scaffolds”. An overview is shown in Figure S4. Firstly, the long reads were used to construct most contigs, while the short reads were used to polish the long-read contigs and supplement sequences missing in the long reads. The long reads were assembled using Flye47 (version: 2.8) with the parameters ‘–meta’ and ‘–pacbio-raw’. Two rounds of Racon (v1.4.10, link https://github.com/lbcb-sci/racon) were then applied to the layouts to obtain the consensus sequences. Two rounds of Pilon48 polishing (v1.23, round 1: “–fix all,amb,circles”, round 2: “–fix all”) were applied to the consensus sequences utilizing the short reads. However, we found that the long reads assemblers failed to assemble the low-abundance genomes in the mock community dataset efficiently (Supplementary Note). To address this issue, the HybridSPAdes17 was used to assemble both short and long reads, and two separate assemblies derived from HybridSPAdes and Flye were used in combination with Quickmerge.49