Mendelian randomization study of whole blood viscosity and cardiovascular diseases.

AIMS: Association between whole blood viscosity (WBV) and an increased risk of cardiovascular disease (CVD) has been reported. However, the causal relationship between WBV and CVD remains not thoroughly investigated. The aim of this study was to investigate the causal relation between WBV and CVD. METHODS: Two-sample Mendelian randomization (MR) was employed, with inverse variance weighting (IVW) as the primary method, to investigate the casual relationship between WBV and CVD. The calculated WBV and medical records of 378,210 individuals participating in the UK Biobank study were divided into halves and analyzed. RESULTS: The means of calculated WBVs were 16.9 (standard deviation: 0.8) and 55.1 (standard deviation: 17.2) for high shear rate (HSR) and low shear rate (LSR), respectively. 37,859 (10.0%) major cardiovascular events (MACE) consisted of 23,894 (6.3%) cases of myocardial infarction (MI), 9,245 (2.4%) cases of ischemic stroke, 10,377 (2.7%) cases of revascularization, and 5,703 (1.5%) cases of coronary heart disease-related death. In the MR analysis, no evidence was found indicating a causal effect of WBV on MACE (IVW p-value for HSR = 0.81, IVW p-value for LSR = 0.47), MI (0.92, 0.83), ischemic stroke (0.52, 0.74), revascularization (0.71, 0.54), and coronary heart disease-related death (0.83, 0.70). The lack of sufficient evidence for causality persisted in other MR methods, including weighted median and MR-egger. CONCLUSIONS: The Mendelian randomization analysis conducted in this study does not support a causal relationship between calculated WBV and CVD.

Comparison of 2 Different Paclitaxel-Coated Balloons in Coronary In-Stent Restenosis: A Randomized Controlled Trial.

Background: Drug-coated balloons (DCBs) offer an effective treatment for in-stent restenosis (ISR). The Genoss DCB is a novel paclitaxel-coated balloon with a shellac plus vitamin E excipient that enhances drug delivery to the target lesion, minimizing restenosis. Objectives: This study aimed to investigate the angiographic efficacy, clinical safety, and effectiveness of the novel shellac plus vitamin E-based DCB in a randomized controlled trial designed to enable regulatory approval of this new device in South Korea. Methods: This noninferiority trial randomized patients experiencing their first ISR to the novel shellac plus vitamin E-based DCB or the reference SeQuent Please iopromide-based DCB in a 1:1 ratio. All patients underwent planned angiographic and clinical follow-up at 6 months. The study was powered for the primary endpoint of 6 months in-segment late lumen loss (LLL). Results: A total of 82 patients from 7 centers were randomized to either the novel shellac plus vitamin E-based DCB group (n = 41) or the reference iopromide-based DCB group (n = 41). The 6-month in-segment LLL was 0.15 ± 0.43 mm with the novel DCB compared with 0.24 ± 0.39 mm with the reference device. The 1-sided 97.5% upper confidence limit of the difference was 0.13 mm, lower than the noninferiority limit of 0.29 mm, achieving noninferiority (P for noninferiority = 0.001). Major cardiovascular events were comparable between 2 groups at 6 months (7.7% for the novel DCB vs 10.3% for the reference DCB; P = 0.692). Conclusions: In this multicenter, head-to-head comparison randomized trial, the novel shellac plus vitamin E-based DCB showed a comparable result to the reference iopromide-based device for the primary endpoint of 6-month in-segment LLL for the treatment of coronary ISR. (Compare the Safety and Efficacy of Genoss® DCB and SeQuent® Please in Korean Patient With Coronary In-stent Restenosis; NCT04405063).

Clinical Outcomes of Drug-Coated Balloon Treatment After Successful Revascularization of de novo Chronic Total Occlusions.

Background: The safety and efficacy of drug-coated balloon (DCB) treatment for de novo coronary chronic total occlusion (CTO) remain uncertain. The aim of this study was to evaluate the outcomes of DCB only treatment for de novo CTO. Methods: In this retrospective study, 101 vessels with de novo CTO lesions dilated by balloon angioplasty with thrombolysis in myocardial infarction flow grade 3 were included. Among them, 93 vessels successfully treated with DCB only treatment were analyzed. The study endpoint was major adverse cardiac events (MACE) at 2 years, a composite of cardiac death, non-fatal myocardial infarction (MI), target vessel revascularization (TVR), and target vessel thrombosis. The secondary endpoint was late lumen loss (LLL) on follow-up coronary angiography. Results: All 84 patients were followed up clinically, and 67 vessels underwent scheduled coronary angiography after 6 months. There were no procedural complications, and three vessels required bailout-stenting. The median follow-up was 720 days (interquartile range [IQR]; 406-1,268 days). MACE occurred in 8.3% of the patients after 1 year, including cardiac death (1.2%), TVR (7.1%), and no non-fatal MI and target vessel thrombosis. Two years after treatment, MACE occurred in 16.7% of the patients, including cardiac death (2.4%), non-fatal MI (3.6%), TVR (13.1%), and no target vessel thrombosis. The mean LLL was 0.03 ± 0.53 mm. Binary restenosis occurred in 14.9% of the treated vessels, and 3.0% of the vessels had late re-occlusion on follow-up coronary angiography. Conclusions: If the result of revascularization using balloon angioplasty is good, the clinical outcomes of DCB only treatment of de novo CTOs at the 2-year follow-up are encouraging, with a low rate of hard endpoints and acceptable MACE rates (Clinical Trial Registration Information; Impact of Drug-coated Balloon Treatment in de novo Coronary Lesion; NCT04619277).

Sex-specific difference of in-hospital mortality from COVID-19 in South Korea.

We sought to assess the impact of sex on in-hospital mortality of patients with COVID-19 infection in South Korea. The study recruited 5,628 prospective consecutive patients who were hospitalized in South Korea with COVID-19 infection, and enrolled in the Korea Centers for Disease Control and Prevention (KCDC) dataset between January 20, 2020, and April 30, 2020. The primary endpoint was in-hospital death from COVID-19. The cohort comprised of 3,308 women (59%) and 2,320 men (41%). In-hospital death was significantly lower in women than men (3.5% vs. 5.5%, hazard ratio (HR): 0.61; 95% confidence interval (CI): 0.47 to 0.79, p <0.001). Results were consistent after multivariable regression (HR: 0.59; 95% CI: 0.41 to 0.85, p = 0.023) and propensity score matching (HR: 0.51; 95% CI: 0.30 to 0.86, p = 0.012). In South Korea, women had a significantly lower risk of in-hospital death amongst those patients hospitalized with COVID-19 infection.

Sex-Related Outcomes of Successful Drug-Coated Balloon Treatment in De Novo Coronary Artery Disease.

PURPOSE: Although drug-coated balloon (DCB) treatment is known to be effective for de novo lesions, the influence of sex on angiographic and clinical outcomes remains unknown. This study aimed to investigate the angiographic and clinical impact of DCB treatment in patients with de novo coronary lesions according to sex. MATERIALS AND METHODS: A total of 227 patients successfully treated with DCB were retrospectively enrolled and divided into two groups according to sex. The primary endpoint was late lumen loss (LLL) at 6-month angiography, and the secondary endpoint was target vessel failure (TVF), which included cardiac death, target vessel myocardial infarction, target lesion revascularization, and target vessel thrombosis. RESULTS: The study enrolled 60 women (26.4%) and 167 men (73.6%). Compared to men, women had a smaller vessel size, larger DCB to reference vessel ratio, and more dissections after DCB treatment (55.0% vs. 37.1%, p=0.016). Women also had a significantly higher LLL compared to men (0.12±0.26 mm vs. 0.02±0.22 mm, p=0.012) at the 6-month follow-up angiography. During a median follow-up of 3.4 years (range 12.7-28.9 months), TVF was similar (women 6.7% vs. men 7.8%, p=0.944). In multivariable analysis, women were independently associated with a higher LLL. CONCLUSION: LLL was higher in women, but there was no difference in TVF between women and men. Based on multivariable analysis, the women sex was an independent predictor of higher LLL (Impact of Drug-coated Balloon Treatment in de Novo Coronary Lesion; NCT04619277).

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates.

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.

A Clinical Risk Score to Predict In-hospital Mortality from COVID-19 in South Korea.

BACKGROUND: Early identification of patients with coronavirus disease 2019 (COVID-19) who are at high risk of mortality is of vital importance for appropriate clinical decision making and delivering optimal treatment. We aimed to develop and validate a clinical risk score for predicting mortality at the time of admission of patients hospitalized with COVID-19. METHODS: Collaborating with the Korea Centers for Disease Control and Prevention (KCDC), we established a prospective consecutive cohort of 5,628 patients with confirmed COVID-19 infection who were admitted to 120 hospitals in Korea between January 20, 2020, and April 30, 2020. The cohort was randomly divided using a 7:3 ratio into a development (n = 3,940) and validation (n = 1,688) set. Clinical information and complete blood count (CBC) detected at admission were investigated using Least Absolute Shrinkage and Selection Operator (LASSO) and logistic regression to construct a predictive risk score (COVID-Mortality Score). The discriminative power of the risk model was assessed by calculating the area under the curve (AUC) of the receiver operating characteristic curves. RESULTS: The incidence of mortality was 4.3% in both the development and validation set. A COVID-Mortality Score consisting of age, sex, body mass index, combined comorbidity, clinical symptoms, and CBC was developed. AUCs of the scoring system were 0.96 (95% confidence interval [CI], 0.85-0.91) and 0.97 (95% CI, 0.84-0.93) in the development and validation set, respectively. If the model was optimized for > 90% sensitivity, accuracies were 81.0% and 80.2% with sensitivities of 91.7% and 86.1% in the development and validation set, respectively. The optimized scoring system has been applied to the public online risk calculator (https://www.diseaseriskscore.com). CONCLUSION: This clinically developed and validated COVID-Mortality Score, using clinical data available at the time of admission, will aid clinicians in predicting in-hospital mortality.

Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling.

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20-96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public's understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.

Polygenic risk score validation using Korean genomes of 265 early-onset acute myocardial infarction patients and 636 healthy controls.

BACKGROUND: The polygenic risk score (PRS) developed for coronary artery disease (CAD) is known to be effective for classifying patients with CAD and predicting subsequent events. However, the PRS was developed mainly based on the analysis of Caucasian genomes and has not been validated for East Asians. We aimed to evaluate the PRS in the genomes of Korean early-onset AMI patients (n = 265, age ≤50 years) following PCI and controls (n = 636) to examine whether the PRS improves risk prediction beyond conventional risk factors. RESULTS: The odds ratio of the PRS was 1.83 (95% confidence interval [CI]: 1.69-1.99) for early-onset AMI patients compared with the controls. For the classification of patients, the area under the curve (AUC) for the combined model with the six conventional risk factors (diabetes mellitus, family history of CAD, hypertension, body mass index, hypercholesterolemia, and current smoking) and PRS was 0.92 (95% CI: 0.90-0.94) while that for the six conventional risk factors was 0.91 (95% CI: 0.85-0.93). Although the AUC for PRS alone was 0.65 (95% CI: 0.61-0.69), adding the PRS to the six conventional risk factors significantly improved the accuracy of the prediction model (P = 0.015). Patients with the upper 50% of PRS showed a higher frequency of repeat revascularization (hazard ratio = 2.19, 95% CI: 1.47-3.26) than the others. CONCLUSIONS: The PRS using 265 early-onset AMI genomes showed improvement in the identification of patients in the Korean population and showed potential for genomic screening in early life to complement conventional risk prediction.

Drug-coated balloon treatment for nonsmall de-novo coronary artery disease: angiographic and clinical outcomes.

OBJECTIVES: Although drug-coated balloons (DCBs) are established for de-novo lesions in small coronary arteries, the impact of DCB treatment according to the reference vessel diameter (RVD) remains poorly defined. This study aimed to evaluate the angiographic and long-term clinical outcomes of DCB treatment for de-novo coronary lesions according to RVD. METHODS AND RESULTS: A total of 227 patients were retrospectively enrolled and stratified according to an RVD >2.5 mm [nonsmall vessel disease (NSVD) group, n = 100] and ≤2.5 mm [small vessel disease (SVD) group, n = 127]. The primary endpoint was late lumen loss (LLL) at a 6-month follow-up, and the secondary endpoint was target vessel failure (TVF, a composite of cardiac death, target vessel myocardial infarction, target vessel revascularization and target vessel thrombosis). The LLL among the 206 patients (90.8%) returning for scheduled angiography at 6 month was similar (NSVD, 0.03 ± 0.22 mm vs. SVD, 0.06 ± 0.25 mm; P = 0.384). TVF was also comparable in both groups at a median follow-up of 3.4 years (NSVD, 7.0 vs. SVD, 7.9 %; P = 0.596). At baseline, there were numerically more dissections in the SVD group compared to the NSVD group (47.2 vs. 35.0 %; P = 0.064); however, most of these had disappeared in both groups at a 6-month follow-up. In a multivariable analysis, the presence of dissection was not associated with LLL or TVF in either group. CONCLUSIONS: The safety and efficacy of DCB treatment for de-novo coronary lesions, in terms of LLL and TVF, was unrelated to RVD.

Impact of Dissection after Drug-Coated Balloon Treatment of De Novo Coronary Lesions: Angiographic and Clinical Outcomes.

PURPOSE: Dissection after plain balloon angioplasty is required to achieve adequate luminal area; however, it is associated with a high risk of vascular events. This study aimed to examine the relationship between non-flow limiting coronary dissections and subsequent lumen loss and long-term clinical outcomes following successful drug-coated balloon (DCB) treatment of de novo coronary lesions. MATERIALS AND METHODS: A total of 227 patients with good distal flow (Thrombolysis in Myocardial Infarction flow grade 3) following DCB treatment were retrospectively enrolled and stratified according to the presence or absence of a non-flow limiting dissection. The primary endpoint was late lumen loss (LLL) at 6-month angiography, and the secondary endpoint was target vessel failure (TVF, a composite of cardiac death, target vessel myocardial infarction, target vessel revascularization, and target vessel thrombosis). RESULTS: The cohort consisted of 95 patients with and 132 patients without a dissection. There were no between-group differences in LLL (90.8%) returning for angiography at 6 months (0.05±0.19 mm in non-dissection and 0.05±0.30 mm in dissection group, p=0.886) or in TVF (6.8% in non-dissection and 8.4% in dissection group, p=0.799) at a median follow-up of 3.4 years. In a multivariate analysis, the presence of dissection and its severity were not associated with LLL or TVF. Almost dissections (93.9%) were completely healed, and there was no newly developed dissection at 6-month angiography. CONCLUSION: The presence of a dissection following successful DCB treatment of a de novo coronary lesion may not be associated with an increased risk of LLL or TVF (Impact of Drug-coated Balloon Treatment in de Novo Coronary Lesion; NCT04619277).

Korean Genome Project: 1094 Korean personal genomes with clinical information.

We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

The whale shark genome reveals how genomic and physiological properties scale with body size.

The endangered whale shark (Rhincodon typus) is the largest fish on Earth and a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 83 animals and yeast. We examined the scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic traits also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: Guanine and cytosine (GC) content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to introns being highly enriched in repetitive elements such as CR1-like long interspersed nuclear elements, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan and showed that the whale shark is a promising model for studies of neural architecture and lifespan.

Decoding a highly mixed Kazakh genome.

We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.

Depression and suicide risk prediction models using blood-derived multi-omics data.

More than 300 million people worldwide experience depression; annually, ~800,000 people die by suicide. Unfortunately, conventional interview-based diagnosis is insufficient to accurately predict a psychiatric status. We developed machine learning models to predict depression and suicide risk using blood methylome and transcriptome data from 56 suicide attempters (SAs), 39 patients with major depressive disorder (MDD), and 87 healthy controls. Our random forest classifiers showed accuracies of 92.6% in distinguishing SAs from MDD patients, 87.3% in distinguishing MDD patients from controls, and 86.7% in distinguishing SAs from controls. We also developed regression models for predicting psychiatric scales with R2 values of 0.961 and 0.943 for Hamilton Rating Scale for Depression-17 and Scale for Suicide Ideation, respectively. Multi-omics data were used to construct psychiatric status prediction models for improved mental health treatment.

The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.

BACKGROUND: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. RESULTS: We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). CONCLUSIONS: Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

The Draft Genome of an Octocoral, Dendronephthya gigantea.

Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ∼276 Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4 Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming.

Sequencing and analysis of the whole genome of Indian Gujarati male.

The article presents the analysis of whole genome sequence of a Gujarati Indian individual (IHGP01) that was sequenced at 23.05× coverage with a total of 74.93 Gb of sequence data generated using Illumina HiSeq 2000 platform. Variant analysis revealed over 3.9 million single nucleotide variants (SNVs) and about 393,000 small insertions and deletions (InDels) including novel variants. The known variants were analyzed for their health and disease relevance and pharmacogenomic profile. Mitochondrial and Y-chromosome haplogroup analysis clearly indicated arrival on the continent not more than 20,000-25,000 years ago, following the route out of Africa to central Europe, then into Asian continent and subsequent migration to West part of the Indian subcontinent. The current research has added 141,000 novel genetic variations to the human DNA database. Functional analysis and validation of these novel variations and revelation of their role in health and disease will add a newer dimension to understand people of this subcontinent.

Investigation of Hanwoo-specific structural variations using whole-genome sequencing data.

BACKGROUND: The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies. OBJECTIVE: TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data. RESULTS: We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages. CONCLUSION: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.

Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia.