MvPPT: a highly efficient and sensitive pathogenicity prediction tool for missense variants

Next generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification. In this study, we developed mvPPT (Pathogenicity Prediction Tool for missense variants), a highly sensitive and accurate missense variant classifier based on gradient boosting. MvPPT adopts high-confidence training sets with a wide spectrum of variant profiles, and extracts three categories of features, including scores from existing prediction tools, allele, amino acid and genotype frequencies, and genomic context. Compared with established predictors, mvPPT achieved superior performance in all test sets, regardless of data source. In addition, our study also provides guidance for training set and feature selection strategies, as well as reveals highly relevant features, which may further provide biological insights of variant pathogenicity.

Genetic assessment of hyperuricemia and gout in Asian, Native Hawaiian, and Pacific Islander subgroups of pregnant women: biospecimens repository cross-sectional study

Background Gout, an inflammatory condition, is characterized by the precipitation of monosodium urate crystals (MSU) in or around distal joints. The latter is caused by chronic hyperuricemia (HU)—high urate levels in the blood. Genetic variations in urate transporters play a significant role in determining urate levels within the human body, rendering some racial and ethnic groups more or less susceptible to developing either HU or gout. This study aims to estimate the frequencies of HU and gout risk alleles in Asian, Native Hawaiian, and Pacific Islander subgroups, using biorepository DNA samples. Methods The biospecimens repository at the University of Hawai’i provided DNA samples of consented post-partum women of Japanese, Filipino, Korean, Native Hawaiian, Samoan, and Marshallese descent. The DNA was previously extracted from maternal blood and genotyped at the Genomics and Bioinformatics Shared Resource, Cancer Center (Honolulu, HI). Nine urate genes: ABCG2, SLC2A9, SLC16A9, GCKR, SLC22A11, SLC22A12, LRR16A, PDZK1, and SLC17A1, were selected due to their significant association with HU and gout risk. Hardy–Weinberg Equilibrium (HWE) for genotype frequencies was assessed, using the Chi-Square test with p < 0.006 for statistical significance. Allele frequencies in our study were then compared to EUR from the 1000 Genomes Project Database Phase III, using Chi-square or Fisher's exact test, when appropriate. Bonferroni correction for multiple comparisons was used, with p < 0.006 for statistical significance. Results Our study involved 1059 post-partum women 18-year-old or older who self-reported their respective race and ethnicity, including Asian, Native Hawaiian, and Pacific Islander ancestry. The Asian subgroups included Japanese, Filipino, and Korean. The Pacific Islander subgroups included Marshallese and Samoan. None of the study participants had a history of gout. We excluded the PDZK1 gene from the final analysis due to its deviation from HWE (p < 0.006) across all the population subgroups, with eight loci remaining for cross-subgroup comparisons. Compared to EUR, the genetic polymorphism frequencies were significantly different-8/8 in Japanese, 6/8 in Korean, 6/8 in Filipino, 8/8 in Samoan, 6/8 in Native Hawaiian, and 6/8 in Marshallese. HU and gout risk alleles indices were 8, 6, 5, 5, 4, and 4 in Japanese, Filipino, Korean, Samoan, Marshallese, and Native Hawaiian, respectively. The percentage of cumulative risk alleles was 100% in both Japanese and Filipino, followed by 83.5% in Korean. Conclusions Compared to EUR, Asian subgroups, particularly Japanese, Filipino, and Korean, had the highest percentage of the cumulative uric acid risk alleles. These results could partly explain the increased risk of developing gout among some Asian ancestral subgroups compared to EUR.

Accumulation and maintenance of information in evolution

Selection accumulates information in the genome - it guides stochastically evolving populations towards states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback-Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright-Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation and recombination. Finally, the cost of maintaining information depends on how it is encoded: specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.

Allele and genotype frequency for milk beta-casein in dairy cattle in the northern region of Tocantins State, Brazil

At present, there is a concern about the quality of milk and diseases related to its consumption, as it can generate discomfort and allergic reactions in some individuals due to its protein components. Thus, the present study was developed to identify the allele and genotype frequencies of genes for β casein, A1 and A2, in dairy herds in the region of Araguaína-TO, Brazil. Genetic material from 421 animals (crossbred dairy cattle in lactation) was used. All animals were numbered for identification, and DNA samples were extracted from hair bulbs. Samples for two markers from the polymorphic regions were characterized and confirmed by real time PCR using the ABI Prism® 7500 Sequence Detection System (Applied Biosystems). Allele and genotype frequencies were determined using the TaqMan™ detection system, where the primer and probe release different fluorescence signals for each allele of the polymorphism. The sampled herd showed frequencies of 28.27% for the A1 allele and 71.73% for the A2 allele. Genotype frequencies were 52.96% (223/421) for A2A2; 37.53% (158/421) for the A1A2 genotype; and 9.50% (40/421) for the A1A1 genotype. The frequency of the A1 allele for β-casein in dairy herds from the northern region of Tocantins was low and is per the results of previous studies. Although the A2A2 genotype of β-casein had a high relative frequency, the A1A2 genotype is still rather frequent, warranting greater selection pressure.

Polymorphism of the genetic determinants of bone mineral metabolism in various groups of the Komi people

The subject of the study is autochthonous population of the Northern and Middle Cis-Urals: Komi-Permyaks, Komi (Zyryans), and Komi-Izhems. The aim of the study is to compare the population frequencies of the LCT (rs4988235) and VDR (FokI rs2228570 and BsmI rs1544410) genes and to consider the contribution of environ-mental and cultural factors to the formation of differences in the genetic determinants of bone tissue metabolism. In total, 181 Komi-Permyak, 223 Komi, and 200 Komi-Izhem subjects were tested clinically and genetically. The evaluation consisted of the determination of polymorphic loci of VDR and LCT genes variants and assessment of clinical and laboratory lactase activity. The information on traditional diet and food composition was obtained from ethnographic materials. The study group of Komi-Izhems differs by a high proportion of C*LCT carriers (0.85) from the other two groups (p < 0.05). The prevalence of hypolactasia, i.e., limited lactase production, is also higher (p < 0.05) in Komi-Izhems (0.64) than in Komi-Permyaks (0.47) and Zyryans (0.41). The T*BsmI allele frequency is higher in Komi-Izems (0.493) in hetero- CT* (0.463) and homozygote TT* (0.261) genotypes, as compared to Zyryans (p < 0.05, where the frequencies are 0.377, 0.329 and 0.212, respectively). The values of BsmI allele and genotype frequencies in Komi-Permyaks are intermediate and do not differ significantly from those in Komi-Izhems and Zyryans. The concentration of T*FokI is highest in Komi-Permyaks (0.528). They are followed by Zyryans (the difference is insignificant, p > 0.05). Komi-Izhems have the smallest proportion of T*FokI allele carriers (0.400) and significantly differ from Komi-Permyaks (p = 0.01). The genotype distributions in FokI locus of VDR in the groups of Komi-Permyaks and Zyryans do not differ, but both show higher CT*FokI genotype frequencies than Komi-Izhems (0.549 and 0.569 against 0.288; p < 0.001). Poor livestock production and a lack of milk in the traditional subsistence economy of the Komi-Permyaks weakened the selection in favor of T*LCT allele and lactase persistence. The low intake of calcium with milk was compensated by an increase in the sensitivity of the target organs to calciferol, the regulator of mineral metabolism, by maintaining the high frequency of carriers of T*BsmI and T*FokI alleles of VDR gene in the population. The more productive dairy farming of Zyryans stimulated selection in favor of lactase persistence. The possibility of continuous consumption of calcium from milk eased the selection pressure on VDR loci. The regulation by T*FokI produced a physiologically sufficient effect and T*BsmI carriership remained low. The diet of the Komi-Izhems, who were accustomed to high-latitude regions, comprised low-lactose dairy products. The population preserved a high carriage of C*LCT and the phenotype of hypolactasia. Moderately intensive selection for vitamin D receptor sensitivity showed up in the increase of VDR T*BsmI frequency only. The high D-vitamin status of the Izhem people was leveraged by the traditional diet with a considerable intake of ergocalciferol-rich venison and fish. The Komi-Permyaks, Komi (Zyryans) and Komi-Izhems occupied different ecological niches and the groups found different ways to adapt to the unfavorable bone-homeorhesis conditions. The flexible responses to the pressure of the environmental factors were imple-mented by the selection of variants of LCT, VDR FokI and VDR BsmI genes, which are located in different chro-mosomes and determine different stages of mineral metabolism. We contend that modern interpopulation differences in distribution of the genotypes and alleles are the manifestations of different strategies of ecological adaptation of anthropologically related groups.

NOTCH4 Single-Nucleotide Polymorphism Is Associated With Brain Arteriovenous Malformation in a Chinese Han Population

Background: Brain arteriovenous malformations (BAVMs) are high-flow intracranial vascular malformations characterized by the direct connection of arteries to veins without an intervening capillary bed. It is one of the main causes of intracranial hemorrhage and epilepsy though morbidity is low. Angiogenesis, heredity, inflammation, and arteriovenous malformation syndromes play important roles in BAVM formation. Animal experiments and previous studies have confirmed that NOTCH4 may be associated with BAVM development. Our study identifies a connection between NOTCH4 gene polymorphisms and BAVM in a Chinese Han population.Methods: We enrolled 150 patients with BAVMs confirmed by digital subtraction angiography (DSA) in the Department of Neurosurgery, Zhujiang Hospital, Southern Medical University from June 2017 to July 2019. Simultaneously, 150 patients without cerebrovascular disease were confirmed by computed tomography angiography/magnetic resonance angiography/DSA. DNA was extracted from peripheral blood and NOTCH4 genotypes were identified by PCR-ligase detection reaction. Chi-square test or Fisher’s exact test was used to evaluate the difference in allele and genotype frequencies between the BAVM group, control group, bleeding, and other complications.Results: Two single-nucleotide polymorphisms (SNPs), rs443198 and rs438475, were significantly associated with BAVM. No SNP genotypes were significantly associated with hemorrhage and epilepsy. SNPs rs443198_ AA-SNP and rs438475_ AA-SNP may be associated with lower risk of BAVM (P = 0.011, OR = 0.459, 95% CI 0.250–0.845; P = 0.033, OR = 0.759, 95% CI 0.479–1.204).Conclusion: NOTCH4 gene polymorphisms were associated with BAVM and may be a risk factor in a Chinese Han population.

Differences in the genotype frequencies of genes related to blood pressure regulation-a comparative study between South-West Europe and Peri-equatorial Africa

Background: Since the emergence of the genus Homo, hominids have occupied a wide variety of environments, facing different selective pressures. Objectives: The aim this study is to compare genotype frequencies between South-West Europe and Peri-equatorial Africa in genes potentially modulators of blood pressure. Methods: The analyzed sample consisted of 325 individuals from Portugal and 226 individuals from Africa (48 from Mozambique and 178 from São Tomé and Príncipe). The following genetic variants were analyzed: intron 4 VNTR in eNOS, rs1050829 in G6PD, -3.7kb α-thalassemic deletion in HBA, rs1800457 in CYB5R3, Hp 1/2 genotype/phenotype in Hp and intron 16 I/D in ACE. Results: Frequencies of genotypes with the 4a allele in eNOS (p<0.001), the G allele in G6PD (p<0.001), the α-3.7 kb in HBA (p <0.001), the C allele in the CYB5R3 (p<0.001) were higher in Peri-equatorial Africa. The Hp 1.1 genotype of Hp has a higher frequency in Peri-equatorial Africa (p=0.002). ACE shows no significant differences. Conclusion: Results show differences in five genetic variants. Conditions of extreme heat and humidity, characteristic of Peri-equatorial Africa, have been associated with increased sodium loss. This study suggests that selected compensatory mechanisms printed in the genome, are nowadays risk factors for hypertension in Peri-equatorial Africa. Keywords: Blood pressure; genetics; Africa.

Genotype Effects on β-Carotene Conversion to Vitamin A: Implications on Reducing Vitamin A Deficiency in the Philippines

Background: The study aimed to identify two beta-carotene 15,15′-monooxygenase (BCMO1) mutations, namely R267S and A379V, and determine their association with vitamin A status among Filipinos 6 to 19 years old respondents of the 2013 Philippine National Nutrition Survey living in the National Capital Region. Materials and Methods: This study followed cross-sectional design. Whole blood specimen was collected in the morning and was used as source of genomic DNA and serum for retinol concentration determination. Fisher exact test was performed to determine whether genotype frequencies were associated to retinol concentrations/vitamin A deficiency status. A level of P < .05 was identified as significant. Results: A total of 693 Filipino children and adolescents were included. Of the 693, there were at least 7.6% who bears the combined mutations for R267S + A379V. Association analysis showed that an inverse relationship exists between the A379V TT variant and vitamin A status. Although the exact role of these identified polymorphisms on retinol/carotenoid metabolism need to be confirmed in dedicated functional studies. Conclusion: This study has identified for the first time the presence of 2 nonsynonymous genetic variants/mutations in the coding region of BCMO1 gene. Interestingly, one of these two variants, the A379V T, was found to be associated with vitamin A status. It is, therefore, warranted to investigate the role of BCMO1 variants for the success of supplementation programs and fortification efforts among vulnerable populations in this region. Genetic variability should be considered for future provitamin A supplementation recommendations among children and adolescents in the Philippines.

NLRP3 Influences Cognitive Function in Schizophrenia in Han Chinese

It has been proposed that immune abnormalities may be implicated with pathophysiology of schizophrenia. The nod-like receptor pyrin domain-contraining protein 3 (NLRP3) can trigger immune-inflammatory cascade reactions. In this study, we intended to identify the role of gene encoding NLRP3 (NLRP3) in susceptibility to schizophrenia and its clinical features. For the NLRP3 mRNA expression analysis, 53 drug-naïve patients with first-episode schizophrenia and 56 healthy controls were enrolled. For the genetic study, a total of 823 schizophrenia patients and 859 controls were recruited. Among them, 239 drug-naïve patients with first-episode schizophrenia were enrolled for clinical evaluation. There is no significant difference in NLRP3 mRNA levels between patients with schizophrenia and healthy controls (p = 0.07). We did not observe any significant differences in allele and genotype frequencies of rs10754558 polymorphism between the schizophrenia and control groups. We noticed significant differences in the scores of RBANS attention and total scores between the patients with different genotypes of rs10754558 polymorphism (p = 0.001 and p &lt; 0.01, respectively). Further eQTL analysis presented a significant association between the rs10754558 polymorphism and NLRP3 in frontal cortex (p = 0.0028, p = 0.028 after Bonferroni correction). Although our findings did not support NLRP3 confer susceptibility to schizophrenia, NLRP3 may be a risk factor for cognitive impairment, especially attention deficit in this disorder.

Prevalence of ABCB1 3435C>T polymorphism in the Cuban population

Objectives ABCB1 gene polymorphisms can modify P-glycoprotein function with clinical consequences. Methods The 3435C>T polymorphism prevalence was analyzed using oligonucleotide probes and next-generation sequencing in 421 unrelated healthy individuals living in Cuba. Data were stratified by gender, ethnic background and residence. The genotype and allelic frequencies were determined. Results The genotype distribution met the Hardy–Weinberg equilibrium assumption. The allelic frequency was 63.5% for the 3435C variant. The genotype frequencies were 41.1% for CC, 44.9% for CT and 14.0% for TT. The allele and genotype distributions differed between individuals living in La Habana and Santiago de Cuba (p<0.05) when ethnic background was analyzed. The allelic distribution was similar among Admixed and Black subjects, and they differed from Caucasians. The CC genotype was equally distributed among Admixed and Black subjects, and they differed from Caucasians. The TT genotype frequency differed between Caucasians and Admixed. The CT genotype was distributed differently among the three groups. Similar distribution was obtained in Brazilians, whereas some similarities were observed in African, Spanish and Chinese populations, consistent with the mixed Cuban ethnic origin. Conclusions This is the first report on allele and genotype frequencies of the 3435C>T polymorphism in Cuba, which may support personalized medicine programs.