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

AbstractBackgroundX - linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in the BTK gene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals.MethodsWe performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed.ResultsAll patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. On structural variant analysis of WGS data, we found a novel large deletion of 5,296 bp at loci chrX:100,624,323-100,629,619 encompassing exons 3-5 of the BTK gene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed mainly South Asian ancestry.ConclusionWhole genome sequencing led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling prenatal diagnosis.

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Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1902510116 ◽

2019 ◽

Vol 116 (18) ◽

pp. 9014-9019 ◽

Cited By ~ 51

Author(s):

Lei Zhang ◽

Xiao Dong ◽

Moonsook Lee ◽

Alexander Y. Maslov ◽

Tao Wang ◽

...

Keyword(s):

B Cell ◽

Whole Genome Sequencing ◽

Single Cell ◽

B Lymphocytes ◽

Genome Sequencing ◽

Somatic Mutations ◽

Whole Genome ◽

Healthy Individuals ◽

Human Lifespan ◽

Increased Risk

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

PLoS Pathogens ◽

10.1371/journal.ppat.1007588 ◽

2019 ◽

Vol 15 (2) ◽

pp. e1007588

Author(s):

Romel D. Mackelprang ◽

Michael J. Bamshad ◽

Jessica X. Chong ◽

Xuanlin Hou ◽

Kati J. Buckingham ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Increased Risk ◽

Extreme Phenotypes ◽

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 frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease

Human Genomics ◽

10.1186/s40246-021-00328-1 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Víctor Raggio ◽

Nicolas Dell’Oca ◽

Camila Simoes ◽

Alejandra Tapié ◽

Conrado Medici ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Diagnosis ◽

Rare Diseases ◽

High Throughput Sequencing ◽

Heart Defects ◽

Large Deletion ◽

Compound Heterozygous ◽

Whole Genome ◽

Artery Disease

Abstract Background Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a high impact on the quality of life and life expectancy of patients, which are in general children or young people. The advent of high-throughput sequencing techniques has improved diagnosis in several different areas, from pediatrics, achieving a diagnostic rate of 41% with whole genome sequencing (WGS) and 36% with whole exome sequencing, to neurology, achieving a diagnostic rate between 47 and 48.5% with WGS. This evidence has encouraged our group to pursue a molecular diagnosis using WGS for this and several other patients with rare diseases. Results We used whole genome sequencing to achieve a molecular diagnosis of a 7-year-old girl with a severe panvascular artery disease that remained for several years undiagnosed. We found a frameshift variant in one copy and a large deletion involving two exons in the other copy of a gene called YY1AP1. This gene is related to Grange syndrome, a recessive rare disease, whose symptoms include stenosis or occlusion of multiple arteries, congenital heart defects, brachydactyly, syndactyly, bone fragility, and learning disabilities. Bioinformatic analyses propose these mutations as the most likely cause of the disease, according to its frequency, in silico predictors, conservation analyses, and effect on the protein product. Additionally, we confirmed one mutation in each parent, supporting a compound heterozygous status in the child. Conclusions In general, we think that this finding can contribute to the use of whole genome sequencing as a diagnosis tool of rare diseases, and in particular, it can enhance the set of known mutations associated with different diseases.

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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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Hypotrichosis with juvenile macular dystrophy: Combination of whole‐genome sequencing and genome‐wide homozygosity mapping identifies a large deletion in CDH3 initially undetected by whole‐exome sequencing—A lesson from next‐generation sequencing

Molecular Genetics & Genomic Medicine ◽

10.1002/mgg3.975 ◽

2019 ◽

Vol 7 (11) ◽

Cited By ~ 1

Author(s):

Amir Hossein Saeidian ◽

Hassan Vahidnezhad ◽

Leila Youssefian ◽

Soheila Sotudeh ◽

Meisam Sargazi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Homozygosity Mapping ◽

Large Deletion ◽

Macular Dystrophy ◽

Whole Genome ◽

Genome Wide ◽

Whole Exome ◽

Generation Sequencing

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Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes

Animal Genetics ◽

10.1111/age.12556 ◽

2017 ◽

Vol 48 (4) ◽

pp. 483-485 ◽

Cited By ~ 14

Author(s):

N. Dürig ◽

R. Jude ◽

H. Holl ◽

S. A. Brooks ◽

C. Lafayette ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Coat Colour ◽

Whole Genome ◽

Deletion Variant ◽

Kit Gene

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Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

Scientific Reports ◽

10.1038/s41598-021-97764-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tatiana Maroilley ◽

Xiao Li ◽

Matthew Oldach ◽

Francesca Jean ◽

Susan J. Stasiuk ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Chromosomal Rearrangements ◽

Large Deletion ◽

Genomic Rearrangements ◽

Model Organisms ◽

Whole Genome ◽

Short Read ◽

C Elegans ◽

Long Read

AbstractGenomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.

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