Additional file 1: of DNA methylation and repressive H3K9 and H3K27 trimethylation in the promoter regions of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, and PD-L1 genes in human primary breast cancer

Table S1. Primer sequences used in this study. (DOCX 18 kb

Additional file 2: of DNA methylation and repressive H3K9 and H3K27 trimethylation in the promoter regions of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, and PD-L1 genes in human primary breast cancer

Figure S1. Methylation PCR and promoter sequences of immune checkpoints and PD-L1 genes. The upper representative blots show gel electrophoresis of the PCR products from NT or TT after bisulfite treatment using methyl primers. Lower figures show the promoter sequences with the primer details (red) and CpG sites (blue) for PD-1 (A), CTLA-4 (B), TIM-3 (C), LAG-3 (D), PD-L1 (E), and TIGIT (F). (PPTX 2479 kb

Genetic polymorphisms of cytochrome P450-1A2 (CYP1A2) among Emiratis

<div><p>Cytochrome P450 1A2 (CYP1A2) is one of the CYP450 mixed-function oxidase system that is of clinical importance due to the large number of drug interactions associated with its induction and inhibition. In addition, significant inter-individual differences in the elimination of drugs metabolized by CYP1A2 enzyme have been observed which are largely due to the highly polymorphic nature of <i>CYP1A2</i> gene. However, there are limited studies on CYP1A2 phenotypes and <i>CYP1A2</i> genotypes among Emiratis and thus this study was carried out to fill this gap. Five hundred and seventy six non-smoker Emirati subjects were asked to consume a soft drink containing caffeine (a non-toxic and reliable probe for predicting CYP1A2 phenotype) and then provide a buccal swab along with a spot urine sample. Taq-Man Real Time PCR was used to determine the CYP1A2 genotype of each individual. Phenotyping was carried out by analyzing the caffeine metabolites using High Performance Liquid Chromatography (HPLC) analysis. We found that 1.4%, 16.3% and 82.3% of the Emirati subjects were slow, intermediate and rapid CYP1A2 metabolizers, respectively. In addition, we found that 1.4% of the subjects were homozygote for derived alleles while 16.1% were heterozygote and 82.5% were homozygote for the ancestral allele. The genotype frequency of the ancestral allele, <i>CYP1A2*1A/*1A</i>, is the highest in this population, followed by <i>CYP1A2 *1A/*1C</i> and <i>CYP1A2 *1A/*1K</i> genotypes, with frequencies of 0.825, 0.102 and 0.058, respectively. The degree of phenotype/genotype concordance was equal to 81.6%. The <i>CYP1A2*1C/*1C</i> and <i>CYP1A2*3/*3</i> genotypes showed significantly the lowest enzyme phenotypic activity. The frequency of slow activity CYP1A2 enzyme alleles is very low among Emiratis which correlates with the presence of low frequencies of derived alleles in <i>CYP1A2</i> gene.</p></div

Additional file 1: of A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement

UCSC genome browser. (DOCX 432 kb

The frequency of <i>CYP1A2</i> alleles among Emiratis in comparison with other populations.

<p>Fig (1A) shows the <i>CYP1A2*1C</i> haplotype frequencies, Fig (1B) shows the <i>CYP1A2*1K</i> haplotype frequencies, Fig (1C) shows the <i>CYP1A2*3</i>, <i>CYP1A2*4</i> and <i>CYP1A2*6</i> haplotypes frequencies, n = sample size, Emiratis (n = 576), Japanese (n = 250), Koreans (n = 150), Chinese (n = 168), African Americans (n = 112), Tunisians (n = 98), Turkish (n = 110), Egyptians (n = 212), Swedish (n = 194), French (n = 100), British (n = 114), Spaniards (n = 117), Saudi Arabians (n = 136), Ethiopians (n = 173).</p

(17MX + 17MU)/137MX ratios vs genotypes.

<p>(17MX + 17MU)/137MX ratios vs genotypes.</p

The <i>CYP1A2</i> genotype frequencies and distribution among Emiratis.

<p>The <i>CYP1A2</i> genotype frequencies and distribution among Emiratis.</p

DataSheet1_Spectrum of genetic variants in bilateral sensorineural hearing loss.docx

Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE).Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families.Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.</p

The frequency of CYP1A2 poor metabolizers among Emiratis in comparison with other populations.

<p>n = sample size, Emiratis (n = 576), Australians (n = 171), Japanese (n = 250), Chinese (n = 78), Americans (n = 101), Italians (n = 95). We did not compare levels of metabolites or their ratios in different studies, but compared rates of ‘poor metabolizers’ or ‘rapid metabolizers’, whatever cut-off points were used in different studies.</p

The majority of the missense mutants in the ZP and intraceullar domains traffic normally to the plasma membrane.

<p>HeLa cells were transiently co-transfected with the C-terminally HA-tagged Endoglin pCMV5 plasmids and the EGFP-tagged H-Ras plasmid and 24 hours later the cells were processed for fluorescence confocal microscopy as described in the methods. The following missense mutanst were shown to traffic predominantly to the plama membrane as eviednced by their co-localization with GFP-H-Ras: C382G ( data not shoiwn due to space limitations), F403S (panles A–C), S407N (not shown), C412S (not shown), G413V (not shown), N423S (panels D–F), R437W (not shown), A452G (not shown), Q476H (not shown), V504M (panels J–L), R571H (panels M–O ) and P615L (panels P–R).</p