Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell–specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

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Whole Genome Rare-Variant Association Study of HIV-1 Progression in a Southern African Population

10.1101/2020.12.16.20248307 ◽

2020 ◽

Author(s):

Prisca K. Thami ◽

Wonderful Choga ◽

Delesa D. Mulisa ◽

Collet Dandara ◽

Andrey K. Shevchenko ◽

...

Keyword(s):

Functional Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rare Variant ◽

Rare Variants ◽

Variant Calling ◽

Analysis Tool ◽

Whole Genome ◽

Host Genetics ◽

Hiv 1

ABSTRACTDespite the high burden of HIV-1 in Botswana, the population of Botswana is significantly underrepresentation in host genetics studies of HIV-1. Furthermore, the bulk of previous genomics studies evaluated common human genetic variations, however, there is increasing evidence of the influence of rare variants in the outcome of diseases which may be uncovered by comprehensive complete and deep genome sequencing. This research aimed to evaluate the role of rare-variants in susceptibility to HIV-1 and progression through whole genome sequencing. Whole genome sequences (WGS) of 265 HIV-1 positive and 125 were HIV-1 negative unrelated individuals from Botswana were mapped to the human reference genome GRCh38. Population joint variant calling was performed using Genome Analysis Tool Kit (GATK) and BCFTools. Cumulative effects of rare variant sets on susceptibility to HIV-1 and progression (CD4+ T-cell decline) were determined with optimized Sequence Kernel Association Test (SKAT-O). In silico functional analysis of the prioritized variants was performed through gene-set enrichment using databases in GeneMANIA and Enrichr. Novel rare-variants within the ANKRD39 (8.48 × 10−8), LOC105378523 (7.45 × 10−7) and GTF3C3 (1.36 × 10−6) genes were significantly associated with HIV-1 progression. Functional analysis revealed that these genes are involved in viral translation and transcription. These findings highlight the significance of whole genome sequencing in pinpointing rare-variants of clinical relevance. The research contributes towards a deeper understanding of the host genetics HIV-1 and offers promise of population specific interventions against HIV-1.

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432. An Outbreak of Coronavirus Disease, 2019 (COVID-19) in a Skilled Nursing Facility – California, 2021: Description, Mitigation, Challenges, and Opportunities

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.632 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S318-S319

Author(s):

Anastasia Maletz ◽

Grace Kang ◽

Raymond Y Chinn ◽

John D Malone ◽

Hosniyeh Bagheri ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Skilled Nursing Facility ◽

Geographic Location ◽

The United States ◽

Infection Prevention And Control ◽

Whole Genome ◽

Nursing Facility ◽

Skilled Nursing ◽

Increased Risk

Abstract Background Skilled nursing facility (SNF) residents comprised 11% of all COVID-19 cases in the United States; however, they account for 43% of deaths with case fatality rates (CFR) of 26.0-33.7%. Methods We report an outbreak of COVID-19, from June 15 to July 21, 2020 in a 159-bed SNF with a staff of 172 that resulted in an infection rate of 97% in residents and 23% in HCWs (Figure 1). A retroactive review outlined mitigation efforts, discussed challenges, identified risk factors among residents and health care workers (HCW) for acquisition of COVID-19, and reviewed opportunities for improvement (Figure 2). Figure 1. Epi Curve of COVID-19 Outbreak in a Skilled Nursing Facility Figure 2. Timeline of COVID-19 Outbreak in a Skilled Nursing Facility Results Factors that contributed to the outbreak: delay in test results had an impact on cohorting; suboptimal adherence to the principles of infection prevention and control (IPC) and minimal adherence monitoring; strict criteria were used to screen for infection; the underappreciated transmissibility of COVID-19 from presymptomatic and asymptomatic persons; symptomatic HCWs who continued to work; the changing guidance on, the suboptimal use of, and an inadequate supply of personal protective equipment; poor indoor air quality due to ventilation challenges; and the important role of community/family/interfacility spread on the outbreak. Whole genome sequencing, performed in 52 samples, identified a common strain that was also found in clusters of 2 other facilities: 1 in the same geographic location, the other in a different geographic location but whose HCWs had the same zip codes as the facility (Figure 3). Certified nursing and restorative nursing assistants had the highest risk of infection with an odds ratio (OR) of 4.02 (confidence interval 1.29-12.55, p value: 0.02) when compared to registered and licensed vocational nurses. The residents’ CFR was 24%. The OR for death was increased by 10.5 (10.20-11.00) for every decade of life as was morbid obesity (BMI > 35) with an OR of 8.50. BMI as a continuous variable increased risk of mortality for every additional unit, OR 1.07 (Tables 1, 2). Whole Genome Sequencing of Isolates from a Skilled Nursing Facility Outbreak Univariate Analysis of Selected Variables Associated with Mortality among Residents at Facility A during COVID-19 Outbreak, June 19 - July 21, 2021 Multivariate Analysis of Factors Associated with Mortality from COVID-19 after Adjusting for Age among Residents (N =124) of Facility A, June 15 - July 21, 2020 Conclusion While implementation of optimal IPC measures in the pre-COVID-19 vaccination era had no impact on the infections in residents who were likely already infected or exposed at the onset of the outbreak, these measures along with non-pharmacologic strategies were effective in halting the spread among HCWs. Disclosures All Authors: No reported disclosures

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Whole‐genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness

Animal Genetics ◽

10.1111/age.12762 ◽

2019 ◽

Vol 50 (2) ◽

pp. 172-174 ◽

Cited By ~ 9

Author(s):

J. Henkel ◽

C. Lafayette ◽

S. A. Brooks ◽

K. Martin ◽

L. Patterson‐Rosa ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Coat Colour ◽

Large Deletion ◽

Whole Genome ◽

Increased Risk

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Whole Genome Sequencing of Four CD34+-Derived iPSC Polycythemia Vera Clones From a Single Female

Blood ◽

10.1182/blood.v120.21.1755.1755 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1755-1755 ◽

Cited By ~ 1

Author(s):

Lifeng Tian ◽

Lucie Piterkova ◽

Linghua Wang ◽

Zhaohui Ye ◽

Linzhao Cheng ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Polycythemia Vera ◽

Cell Lines ◽

Genome Sequencing ◽

Genome Analysis ◽

Blood Cells ◽

Somatic Mutations ◽

Germline Mutations ◽

Whole Genome ◽

Increased Risk

Abstract Abstract 1755 Polycythemia vera (PV) is an acquired clonal hematopoietic disorder characterized by the JAK2V617F somatic mutation, which, however, constitutes only a variable part of the PV clone. Even within the JAK2V617F subclone, heterozygous and homozygous JAK2V617F progenitors coexist. Further, family clustering of PV suggests the existence of predisposing germline mutations. The nature of these pre-JAK2V617Fsomatic and germline mutations has not yet been identified, and the search for these predisposing genetic lesions using marrow and blood cells is hampered by their genetic heterogeneity. In order to overcome this obstacle, we generated 5 inducible pluripotent stem cell lines (iPSC) from the same PV female with different JAK2 genomic configuration (4 from CD34+ blood cells, one from marrow mesenchymal cells having germ-line DNA configuration). Genomic DNA was isolated from the cell lines, followed by whole genome sequencing (WGS) at >20X depth, and whole exome sequencing (WES) at >130X depth. We have developed a comprehensive WGS/WES pipeline for sequence alignment and variant calling. The major components are: a) Pre-processing and quality control of raw reads outputted from sequencing instruments; b) Align the read against the Human Genome Project reference using BWA (Burrows-Wheeler Aligner); c) Local realignment at indels using GATK (Genome Analysis Toolkit); d) Identify germline/somatic single nucleotide variants (SNVs), copy number variants (CNV) and structural variants (SV) using GATK, Varscan2, Breakdancer, CNVnator, and Pindel. The variant calls are intersected and merged. Calls detected by two or more algorithms are regarded as high confidence. Two somatic mutations, rs1047840, and rs3795677 were identified by WGS and WES in the CD34+ cell derived iPSCs. rs1047840 (E589K) is a SNP in EXO1 gene that encodes a protein with 5' to 3' exonuclease activity as well as an RNase H activity. EXO1 is involved in DNA mismatch repair and homologous recombination. rs1047840 conferred increased risk of breast, lung, and gastric cancer. rs3795677 (R64H) is a SNP in FMN2 gene, which is required for microtubule-independent chromatin positioning during metaphase. Interestingly, these two mutations are all common SNVs, and they are located in a duplicated region on 1q43. Whole genome analysis is ongoing to characterize and validate the complex mixture of SVs in this region, identify potential translocations and determine the exact genomic breakpoints. The variants will be validated in non-iPSC cells from the same individual to rule out iPSC artifacts. This work identifies somatic mutations in EXO1 and FMN2, and CNVs in 1q43 as the potential genetic defects involved in the early pathogenesis of PV. It also demonstrates the value of combining WGS and WES for the identification of somatic mutations. Disclosures: No relevant conflicts of interest to declare.

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Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota

10.1101/544502 ◽

2019 ◽

Author(s):

Kaisa Thorell ◽

Linn Inganäs ◽

Annette Backhans ◽

Lars Agréus ◽

Åke Öst ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Amplicon Sequencing ◽

Population Based ◽

Whole Genome ◽

Pathogenic Potential ◽

Human Microbiota ◽

16S Amplicon Sequencing ◽

Increased Risk ◽

Brachyspira Aalborgi

AbstractColonic spirochaetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance and only few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. In these individuals, 17 (2.3 %) had colonic spirochaetosis, which was associated with eosinophilic infiltration and a three-fold increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochaetosis we successfully isolated, cultured and performed whole genome sequencing of in total 17 isolates including theBrachyspira aalborgitype strain 513AT. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and non-spirochaetosis controls.This is the first report of whole genome analysis of clinical isolates from individuals with colonic spirochaetosis. We found one isolate to be of the speciesBrachyspira pilosicoliand all remaining isolates were of the speciesBrachyspira aalborgi. Besides displaying extensive genetic heterogeneity, the isolates harboured several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies fail to detectBrachyspiradue to primer incompatibility. This failure to detect colonic spirochaetosis should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.

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Genome-wide association study using whole-genome sequencing to identify a novel locus associated with cardiomyopathy risk in adult survivors of childhood cancer: Utility of a two-stage analytic approach.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.1516 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 1516-1516

Author(s):

Yadav Sapkota ◽

Qi Liu ◽

Kyla C. Shelton ◽

Xuexia Wang ◽

Carmen Louise Wilson ◽

...

Keyword(s):

Cancer Survivors ◽

Childhood Cancer ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Childhood Cancer Survivors ◽

Whole Genome ◽

Genome Wide ◽

Increased Risk ◽

Survivors Of Childhood Cancer ◽

Genome Wide Significance

1516 Background: Survivors of childhood cancer are at increased risk of treatment-related cardiomyopathy, found to be modified by genetic factors. To further investigate genetic risks of cardiomyopathy, we utilized whole-genome sequencing (WGS) in a clinically phenotyped cohort of long-term survivors of pediatric cancer. Methods: Utilizing a novel 2-stage analytic approach, we first performed association analysis for ejection fraction (EF) using WGS data in European-descent childhood cancer survivors from the St. Jude Lifetime Cohort (SJLIFE). EF was analyzed as a continuous variable to increase statistical power for genetic discovery. Common variants (minor allele frequency (MAF) > 0.05) were analyzed using linear regression, adjusting for age at diagnosis, sex, age at follow-up, doses of anthracycline and average radiation dose to the heart, and eigenvectors. Rare/low-frequency variants were aggregated by different functional annotations and agnostic 4-kb sliding windows, testing jointly using Burden/SKAT test. In the second stage, only the variant showing genome-wide significance with EF was tested for its association with cardiomyopathy risk. Results: Among the 2,015 SJLIFE survivors with WGS data, a locus on 6p21.2 near KCNK17achieved genome-wide significance with EF (rs2815063; MAF = 0.13; per allele beta = -0.016; P = 2.10´10-8), which replicated in 320 SJLIFE African survivors (MAF = 0.48; beta = -0.015; P = 0.004). In SJLIFE Europeans, 282 had a CTCAE Grade 2-5 cardiomyopathy. rs2815063 was significantly associated with increased risk of cardiomyopathy [per allele odds ratio (OR) = 1.38; P = 0.02], which replicated in 3,957 European survivors from the Childhood Cancer Survivor Study (163 CTCAE Grade 3-5 self-reported cases; per allele OR = 1.39; P = 0.038). rs2815063 alters DNA binding motif of EWSR1-FLI1, whose expression was found to lead to cardiomyopathy and death due to chronic cardiac failure in mice. Conclusions: Using a 2-stage approach, we report a novel locus for cardiomyopathy in childhood cancer survivors, which warrants additional work to gain mechanistic insights.

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Comprehensive analysis of GBA using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing

10.1101/2021.11.12.21266253 ◽

2021 ◽

Author(s):

Marco Toffoli ◽

Xiao Chen ◽

Fritz J Sedlazeck ◽

Chiao-Yin Lee ◽

Stephen Mullin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Short Read ◽

Increased Risk ◽

Long Read

GBA variants cause the autosomal recessive Gaucher disease, and carriers are at increased risk of Parkinson disease (PD) and Lewy body dementia (LBD). The presence of a highly homologous nearby pseudogene (GBAP1) predisposes to a range of structural variants arising from either gene conversion or reciprocal recombination, the latter resulting in copy number gains or losses, complicating genetic testing and analysis. To date, short-read sequencing has not been able to fully resolve these or other variants in the key homology region, and targeted long-read sequencing has not previously resolved reciprocal recombinants. We present and validate two independent methods to resolve recombinant alleles and other variants in GBA: Gauchian, a novel bioinformatics tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore long-read sequencing after enrichment with appropriate PCR. The methods were concordant for 42 samples including 30 with a range of recombinants and GBAP1-related mutations, and Gauchian outperforms the GATK Best Practices pipeline. Applying Gauchian to Illumina sequencing of over 10,000 individuals from publicly available cohorts shows that copy number variants (CNVs) spanning GBAP1 are relatively common in Africans. CNV frequencies in PD and LBD are similar to controls, but gains may coexist with other mutations in patients, and a modifying effect cannot be excluded. Gauchian detects a higher frequency of GBA variants in LBD than PD, especially severe ones. These findings highlight the importance of accurate GBA mutation detection in these patients, which is possible by either Gauchian analysis of short-read whole genome sequencing, or targeted long-read sequencing.

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