Significance Of Genetic Variants Research Articles

An insertion variant of MGMT disrupts a STAT1 binding site and confers susceptibility to glioma

BackgroundO6-methylguanine-DNA methyltransferase (MGMT) is a pivotal enzyme for repairing DNA alkylation damage. Epigenetic modification of MGMT has been well known as a promising prognostic biomarker for glioma. However, the significance of genetic variations of MGMT in glioma carcinogenesis has not been fully elucidated.MethodsThe associations between expression quantitative trait loci (eQTLs) of MGMT and glioma susceptibility were evaluated in a case–control study of 1056 individuals. The function of susceptibility locus for glioma was explored with a set of biochemical assays, including luciferase reporter gene, EMSA and supershift EMSA, ChIP, and siRNA knockdown.ResultsWe found that rs11016798 TT genotype was associated with a significantly decreased risk of glioma (OR = 0.57, 95% CI 0.39–0.85; P = 0.006). Stratification analyses indicated that the association between rs11016798 and glioma was more pronounced in males (OR = 0.62, 95% CI 0.40–0.97; P = 0.035), older subjects (OR = 0.46, 95% CI 0.27–0.80; P = 0.006), WHO grade IV glioma (OR = 0.58, 95% CI 0.35–0.96; P = 0.033), and IDH wildtype glioma (OR = 0.43, 95% CI 0.21–0.88; P = 0.022). We characterized an insertion variant rs10659396 in the upstream of MGMT as a causative variant. The risk allele rs10659396 ins allele was demonstrated to downregulate MGMT expression by disrupting a STAT1 binding site. Knockdown of STAT1 remarkably attenuated MGMT expression. Moreover, the rs10659396 allele-specific positive correlation was observed between the expression of STAT1 and MGMT in population.ConclusionsThe study demonstrates that an insertion variant of MGMT rs10659396 confers susceptibility to glioma by downregulating MGMT expression through disrupting a STAT1 binding site.Graphic abstract

The Influence of Genetic Variations and Drug Interactions Based on Metabolism of Antidepressants and Anticonvulsants.

The variability in drug response is highly complex and can be attributed to the polymedication, genetic polymorphisms modulating drug-metabolizing enzyme activities (cytochromes P450, CYP), physiological and environmental factors." sentence could be revised as "The variability in drug response is highly complex and can be attributed to the polymedication, genetic polymorphisms modulating drugmetabolizing enzyme activities (cytochromeP450s (CYP)), physiological and environmental factors. The main objective of this review is to deeply discuss the role of biotransformation in the occurrence of antidepressant and anticonvulsant induced inter individual variabilities with the focus on genetic variations and drug interactions. An extensive search of the literature has been conducted related to biotransformation of the antidepressant and anticonvulsant agents on relationships between genetic differences and drug interactions on available databases. Following keywords are used for relevant articles: "metabolic enzyme", "pharmacokinetic", "antidepressant", "anticonvulsant", "genetic variations", "enzyme inhibition", "enzyme induction" and also with a list of all included antidepressant and anticonvulsants. In the present review, we provided an overview of documented clinically significant pharmacokinetic drug interactions, physiological and environmental differences. We further discuss the significance of genetic variations in drug metabolizing enzymes to underline the need for using the information on both genotype and drug interactions towards implementing better clinical outcomes through personalized medicine in neurology and psychiatry. The present review clearly illustrates that interindividual differences in the biotransformation (including genetic variability of the drug metabolizing enzymes, age, sex, diet) of the antidepressant and anticonvulsant drugs, which are commonly prescribed medications globally, has a crucial role in the occurrence of adverse effects and various drug responses. Therefore, the potential results of the drug-drug interactions and individual genetic characteristics should always be considered to make pharmacotherapy safer and more effective, as they have major clinical implications.

The 2021 FASEB virtual Catalyst Conference on Transplantation Genomics: Ethics of Research and Clinical Applications, January 27, 2021.

The 2021 FASEB virtual Catalyst Conference on Transplantation Genomics: Ethics of Research and Clinical Applications, January 27, 2021.

The possible influence of genetic aetiological factors on molar–incisor hypomineralisation

ObjectiveThe present study searched for evidence of possible associations between some genetic factors that could affect the development of molar–incisor hypomineralisation (MIH). MethodsIn 113 patients who were surgically treated at an Otorhinolaryngology and Cervicofacial Surgery Clinic (ORL) during early childhood, human leukocyte antigen (HLA) DQ2 and DQ8 haplotypes and single nucleotide polymorphisms (SNP) of eight amelogenesis-related genes were searched in genomic DNA. Genotypes were determined by high resolution melting (HRM), TaqMan genotyping assays, and Sanger sequencing. Association between MIH and the HLA DQ2 and DQ8 alleles was tested using a univariate logistic regression. The significance of genetic variants was analysed using the Cochran–Armitage tests for trend and the Fisher exact tests. ResultsWe identified MIH in 22 (19.5 %) of the 113 children. Among the evaluated genetic variants, SNP rs2245803 in the MMP20 gene in a homozygous form in a recessive model was associated with MIH development (OR, 2.796; 95 %CI, 1.075 − 4.783; p = 0.0496) with the genotype distribution of TT(3), TG(6) or GG(13) in children with MIH and distribution of TT(18), TG(42) or GG(31) in children without MIH. ConclusionsWhile the aetiology of MIH remains unclear, our findings suggest that variants of genes associated with amelogenesis may play important roles in susceptibility to MIH.

Protecting essential information about genetic variants as trade secrets: a problem for public policy?

ABSTRACTIn 2013, the U.S. Supreme Court held that naturally occurring human genes are not patentable subject matter. This decision, invalidating patents held by Myriad Genetics involving genes affecting breast cancer, appeared to further the constitutional policy behind intellectual property protection to promote scientific progress and to make genetic testing more readily available to patients. However, the decision's ironic aftermath is continuing assertion by genetic testing companies of trade secrets protections over information about the significance of genetic variants.This article analyzes possible approaches to the assertion of trade secret protections over information about the significance of genetic variants. Specifically, we consider five approaches: voluntary responses from the scientific community; Food and Drug Administration (FDA) or CMS regulation; creation of additional march-in rights as under the Bayh Dole Act; compulsory licensing as under patent law; and creation of a public policy exception to trade secret protection. We explore what each approach would require legally if applied to break trade secret barriers, together with their advantages and disadvantages. While our analysis concerns genetic information, we conclude with some thoughts about its relevance to other types of big data now protected by trade secrets such as information about innovations in quality of care.

Significance of genetic variations in developmental enamel defects of primary dentition in Polish children

ObjectivesThe aim of the study was to reveal the association between developmental defects of enamel (DDE) and single nucleotide polymorphisms (SNPs) in the ENAM, AMELX, AMBN, TUFT1, and TFIP11 genes.Material and methodsThe molecular analysis was carried out in 52 children, aged 10–42 months, from four nursery schools situated in the region of Poznan, Poland (26 individuals with hypomineralization and/or hypoplasia of enamel - “cases” and 26 unaffected children - “controls”), chosen from 262 individuals that had prior dental examination. Six selected SNP variants (rs17878486 in AMELX, rs4694075 in AMBN, rs3796704 in ENAM, rs134136 and rs5997096 in TFIP11, and rs3790506 in TUFT1) were genotyped by the TaqMan probes assay. Genotype and allele frequencies were calculated, and a standard chi-squared analysis was used to test for deviation from Hardy-Weinberg equilibrium. The association between genetic variations and developmental defects of enamel was assessed by the Fisher’s exact test and p ≤ 0.05 was considered statistically significant.ResultsStatistically significant positive correlations were found between the rare T allele (p = 0.005) and the TT genotype (p = 0.0052) for rs17878486 in AMELX and occurrence of developmental enamel defects in primary dentition of children. For rs4694075 in AMBN, a higher incidence of the rare T allele (p = 0.0157) was observed in controls compared to DDE cases, whereas the wild-type CC homozygote was more frequent in DDE cases than in controls (p = 0.0062).ConclusionsThe study showed that the single nucleotide polymorphisms in the AMELX and AMBN genes may be genetic variants that contribute to developmental defects of enamel in primary dentition of children.Clinical relevanceThe single nucleotide polymorphisms of enamel formation genes may increase the risk for developmental defects of enamel (DDE) occurrence in primary dentition in children.

Association of PIK3CA H1047R and STK11 F354L mutations with response to neoadjuvant chemoradiotherapy and survival in esophageal cancer.

55 Background: Neoadjuvant chemoradiotherapy is the standard treatment for locally advanced esophageal cancer. However, its efficacy is limited in non-responders and there is no reliable clinical parameter in predicting treatment response. We aim to identify chemoradiation-resistant cancers and avoid unnecessary treatments in non-responders with mutation analysis. Methods: Genomic DNA was extracted from diagnostic biopsy specimens of 20 patients (10 with good and 10 with poor response) with esophageal squamous cell carcinoma after neoadjuvant chemoradiotherapy and esophagectomy. Using next-generation sequencing, we screened mutation hotspots in 46 cancer-related genes (Ion AmpliSeq Cancer Panel). Potential predictive genetic variations were validated in another cohort of patients. Chemoradiotherapy response was based on pathological evaluation of surgically resected specimens. The prognostic significance of genetic variations was evaluated with Cox regression survival analysis. Results: In the first cohort, we discovered PIK3CA H1047R and STK11 F354L as potential targets to predict chemoradiation resistance. Next, we investigate these genetic variations in another 54 patients. Altogether, 18.9% (14/74) and 6.8% (5/74) of patients had PIK3CA H1047R and STK11 F354L, respectively. In patients with poor response to chemoradiotherapy, 45.8% (11/24) had either PIK3CA H1047R or STK11 F354L; compared to 12.0% (6/50) in patients with good response ( p = 0.001). In other words, 64.7% of patients with either one genetic variation responded poorly to chemoradiotherapy. In survival analysis, the 5-yr survival rates were 7.7% and 43.7% in patients with either one genetic variation and those without, respectively ( p = 0.003). In multivariable analysis, the presence of either one genetic variation was a significant prognostic factor for overall survival (Hazard ratio: 2.43, 95% confidence interval: 1.195-4.944, p= 0.014). Conclusions: PIK3CA H1047R and STK11 F354L mutations are associated with poor response to neoadjuvant chemoradiotherapy and worse prognosis in esophageal cancer. It may potentially be biomarkers to guide treatment decisions.

Abstract A2-38: Interpretation and classification system for somatic variants identified in solid tumor molecular profiling

Abstract Variant classification schemes for clinical laboratory reporting of inherited variants from molecular diagnostic tests for germline conditions have been widely published. These group variants by pathogenicity, distinguishing benign variants from those known or likely to be pathogenic. In contrast, there are no published schemes for somatic variant classification in acquired cancer. Factors such as histology, cancer type and actionability must be considered to determine the variant's clinical significance. We present a somatic variant classification scheme based on our experience in solid tumor molecular profiling using next-generation sequencing (NGS). Our protocol for somatic variant assessment from solid tumor NGS molecular profiling is comprised of: a) Determination of frequency of the variant in population databases, b) Information gathering on the variant from publicly available databases, c) Functional prediction using in silico tools for missense variants, d) Literature searches for publications relevant to variant function and actionability in the context of tumor type. Grading of Recommendations Assessment, Development and Evaluation (GRADE) principles are applied to determine whether evidence is sufficient to classify a given variant based on actionability. We applied this protocol to classify a pilot set of 258 variants in 158 consecutive patients tested using NGS. We present a classification system to interpret significance of genetic variants in molecular analysis of cancer, utilizing key factors: a) known or predicted pathogenicity of the variant; b) primary site and tumor histology in which the variant is found; c) whether the variant is recurrent in the specific gene; and, d) evidence of clinical actionability for patient management including targeted therapies. We used these factors to develop a 5-category Somatic Variant Classification scheme, for simplified reporting of variant interpretations to treating oncologists. Using this system, we classified 258 variants identified in 158 patients tested using NGS, and evaluated factors impacting the classification. In addition to the subset of findings with known clinical significance (37% of variants), a majority of the findings were potentially clinically actionable by extrapolating from evidence in other tumour types and recurrent variants of the same gene (49%). Classification depended on: Definition of “actionability”; primary tumor site and histology; level and type of evidence available; and, variant frequency. The pathogenicity of a specific gene/variant was distinct from its actionability; although both were indicative of biological relevance, only the latter informed patient management. By focusing on actionability, the SVC attempts to gauge the impact of genomic findings on patient management and care, bringing the most clinically relevant findings to the forefront of a list identified by NGS. Our Somatic Variant Classification scheme uses objective criteria to provide a structured stratification of the clinical significance of a somatic variant in a given histopathology, for a given patient, and for guiding laboratory procedures with respect to reporting. The distinction between “actionability” and “pathogenicity,” and the relevance of the former to the oncology setting, distinguishes our proposed categorization system from previously published classifications. The SVC can be applied to genomic datasets using various detection platforms, to track over time how advances in the field and new knowledge are affecting clinical care. This classification system enables an objective assessment over time of the relationship between available genomic information and the number of actionable findings which may impact patient care. Citation Format: Mahadeo A. Sukhai, Mariam Thomas, Kenneth J. Craddock, Tong Zhang, Tracy L. Stockley, Suzanne Kamel-Reid. Interpretation and classification system for somatic variants identified in solid tumor molecular profiling. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-38.

Significance of genetic variants in DLC1 and their association with hepatocellular carcinoma

DLC1 has been shown to be downregulated or absent in hepatocellular carcinoma (HCC) and is associated with tumorigenesis and development. However, only a small number of studies have focused on genetic variations of DLC1. The present study performed exon sequencing for the DLC1 gene in HCC tissue samples from 105 patients to identify functional genetic variation of DLC1 and its association with HCC susceptibility, clinicopathological features and prognosis. A novel missense mutation and four non-synonymous single nucleotide polymorphisms (SNPs; rs3816748, rs11203495, rs3816747 and rs532841) were identified. A significant correlation of rs3816747 polymorphisms with HCC susceptibility was identified. Compared to individuals with the GG genotype of rs3816747, those with the GA (odds ratio (OR)=0.486; P=0.037) or GA+AA genotype (OR=0.51; P=0.039) were associated with a significantly decreased HCC risk. Furthermore, patients with the GC+CC genotype of rs3816748, the TC+CC genotype of rs11203495 or the GA+AA genotype of rs3816747 had small-sized tumors compared with those carrying the wild-type genotype. No significant association of DLC1 SNPs with the patients' prognosis was found. These results indicated that genetic variations in the DLC1 gene may confer a risk for HCC.

EGFL7 polymorphism to predict tumor response in metastatic colorectal cancer (mCRC) patients (pts) treated with FOLFIRI and bevacizumab (BV).

3565 Background: Angiogenesis involves endothelial cell (EC) sprouting, proliferation, and differentiation and recruitment of mural cells to stabilize new vessels. The proteins Epidermal Growth Factor Domain-Like 7 (EGFL-7) and Activin Receptor-like Kinase 1 (ALK1) play critical roles. EC-secreted EGFL7 antagonizes Notch to promote EC proliferation, sprouting, and motility. EGFL7 also regulates mural cell recruitment and extracellular matrix deposition. ALK1 is an EC-restricted TGF-β Type 1 receptor with downstream repression of Vascular Endothelial Growth Factor (VEGF) signaling. ALK1 also promotes pericyte-EC adhesion. EGFL7 or ALK1 inhibition enhances antitumor efficacy when combined with BV in murine models. Both are overexpressed in many cancers and may be critical for efficacy of anti-VEGF therapy. We tested whether EGFL7 (rs1051851, rs2297538) and ALK1 polymorphisms (rs2293094, rs11169953, rs706819) will predict efficacy of BV-based therapy in mCRC pts. Methods: Genomic DNA was extracted from peripheral whole blood samples from 455 mCRC pts treated with first-line BV and FOLFIRI. SNPs were analyzed by PCR-based direct DNA sequencing and evaluated for association with tumor response rate (RR), overall survival (OS), and progression free survival (PFS). Results: Male/female: 272/183; median age: 62 (range: 25-81); median PFS and median OS: 10.9 (95%CI: 10.1-11.6) and 29.9 (95%CI: 25.9-34.6) months, respectively; response to therapy: 59% (215 pts); median follow-up:23.6 (range: 1.8-60.4) months. Pts carrying the EGFL7 rs1051851 G/G alleles had a 62% RR versus 56% in pts with A/G and 29% in patients with A/A (p=0.0130, Cochran-Armitage trend test). The result remained significant after adjustment for baseline pt characteristics (p=0.026, Multivariable logistic regression test). There was no statistically significant association between tested polymorphisms and OS or PFS. Conclusions: The EGFL7 SNP rs1051851 may predict tumor response in mCRC pts treated with FOLFIRI and BV. To our knowledge, this is the first study demonstrating predictive significance of genetic variations in EGFL7. Prospective validation of this study is warranted.

New prognostic loci related to the survival of patients with advanced non-small cell lung cancer receiving chemotherapy: A genome-wide association study.

e18119 Background: We investigated prognostic significance of genetic variants identified by genome-wide association study (GWAS) for the patients with advanced non-small cell lung cancer (NSCLC). Methods: Among the patients included in our previous GWAS paper for lung cancer risk, we selected 348 patients with stage IV NSCLC, who had started chemotherapy in May 2002 through December 2005 at the National Cancer Center Hospital, and had the follow-up data available. After applying quality control criteria, the association of 271,817 genotyped SNPs with overall survival was analyzed by the Cox proportional hazard regression model adjusted with known prognostic factors using the bootstrap resampling procedure. Results: Overall, the median age of patients was 56 years, 64.9% were female, 67.2% were never smokers, and 80.4% had adenocarcinoma; 73.0% received platinum-based chemotherapy and 73.6 % received EGFR-TKIs. The median survival time (MST) for all patients was 25 months. A total of 23 SNPs with MAF of >0.05 were selected using a cut-off minimum p-value of <5x10-5 (either in additive or dominant models) in at least 70% of a thousand bootstrap samples. Those SNPs were known to be located in the genomic coding region of the FAM154A, EGF, NCOA2, CDH8, ANKS1A, DLST, VGCNL1, SLC35D2, and THSD7B. Carrying a variant genotype of rs1571228 SNP located on the FAM154A, for example, was significantly associated with better overall survival with MST of 29.6 months for those with AG/GG (n=144/30) genotypes vs. 21.5 months for those with AA (n=173) genotype under the dominant model (hazard ratio of 0.52 [95% CI, 0.42-0.67], p = 2.03 x 10-7). This association remained consistent in a subgroup of patients who received platinum-based chemotherapy (n= 254, p = 1.69 x 10-6) or EGFR-TKIs (n = 256, p = 9.04 x 10-6). Conclusions: Genetic variants at multiple loci were found to be prognostically important for patients with advanced NSCLC, which warrants further investigation into its biological relevance and clinical implication.

Clinical significance of genetic variations in the PI3K/PTEN/AKT/mTOR pathway in Korean patients with colorectal cancer.

628 Background: Signaling through the PI3K/PTEN/AKT/mTOR pathway is responsible for balancing cell survival and apoptosis. Accordingly, the present study analyzed 14 SNPs of the PI3K/PTEN/AKT/mTOR pathway genes and their impact on the prognosis for patients with colorectal cancer. Methods: Four hundred and forty-four consecutive patients with surgically resected colorectal adenocarcinoma were enrolled in the present study. The genomic DNA was extracted from fresh colorectal tissue and 14 polymorphisms of the PI3K/PTEN/AKT/mTOR pathway genes determined using a real-time PCR genotyping assay. Results: Pathologic stages after surgery were as follows: stage 0/I (n=85, 19.1%), stage II (n=149, 33.6%), stage III (n=147, 33.1%), and stage IV (n=63, 14.2%). Univariate and multivariate survival analysis including stage, age, site of disease, adjuvant chemotherapy, and CEA level showed that these polymorphisms were not associated with progression-free or overall survival. For the clinicopathologic parameters, CEA level and TNM stage were significant prognostic factors in a Cox model for survival. Conclusions: None of the 14 SNPs of the PI3K/PTEN/AKT/mTOR pathway genes investigated in this study was found to be an independent prognostic marker for Korean patients with surgically resected colorectal cancer. No significant financial relationships to disclose.

Several interleukin-4 and interleukin-13 gene single nucleotide polymorphisms among Chinese asthmatic patients

Asthma is a common respiratory disease associated with airway hyperactivity and high total serum immunoglobulin E (IgE) levels. The asthmatic phenotypes are widely considered to be caused by environmental effects on genetically predisposed individuals. Interleukin (IL)-4 and IL-13 act on B cells and regulate the IgE production, and the single nucleotide polymorphisms (SNPs) in the IL-4 and IL-13 genes are implicated in the pathogenesis of asthma. To study the association of IL-4 and IL-13 gene polymorphisms with asthma, we sequenced the promoter regions and exons of IL-4 and IL-13 genes in two groups: one (spouses group) consisted of 13 pairs of asthmatic patients (cases) and their unaffected spouses (controls); the other (parents group) consisted of 11 pairs of asthmatic children (cases) and their unaffected father/mother (controls). In total, seven polymorphisms were identified, one novel and six previously reported. However, according to the results of the statistical analysis we performed, no statistically significant association of these SNPs and asthma was observed (p > 0.05). Asthma is largely determined by the accumulation of several certain genetic variations other than one or two SNPs. Future function studies may be able to help us reveal the significance of genetic variants we identified in this study.

Pharmacogenetics of a PARP inhibitor ABT-888 metabolic pathway

e14556 Background: Poly(ADP-ribose) polymerase (PARP) is essential for single-stranded DNA break repair and repair of DNA damage can lead to radio- and chemo-resistance. Thus, inhibition of PARP activity can sensitize cells to cytotoxic therapies. ABT-888 is a potent, orally bioavailable PARP inhibitor. Preclinical studies suggest that ABT-888 potentiates multiple cytotoxic agents and its efficacy is correlated with plasma/tumor drug concentrations. The objective of this study was to determine the pharmacogenetic effect of genetic variants in the ABT-888 metabolic pathway, with the aim to better understand molecular basis of the variation in ABT-888 pharmacokinetics (PK) and therapeutic outcome. Methods: The major enzymes responsible for ABT-888 metabolism were identified by in vitro metabolism studies with specific recombinant human cytochrome P450 (CYP) enzymes. The functional significance of genetic variants of the identified enzymes was assessed by examining ABT-888 metabolic kinetics by candidate variant enzymes and microsomes. The association of the functional significant genetic variants with the PK and clinical outcome is being evaluated in the context of an ongoing phase I trial in which ABT-888 is administered in combination with irinotecan in patients with advanced solid tumors. Results: ABT-888 was metabolized predominantly by human CYP2D6, to a less extent by CYP1A1, and to a negligible extent by CYP1A2, 2C9, 2C19, 3A4, and 3A5. CYP2D6*10 exhibited markedly reduced catalytic capability in ABT-888 overall metabolism and the metabolite (A-925088) formation, with in vitro maximum clearance being 31% and 5.3%, respectively, of that estimated from the wild-type CYP2D6. In human liver microsomes carrying homozygous CYP2D6*4, the rates of parent drug disappearance and metabolite formation were significantly lower than those observed in the microsomes carrying wild-type CYP2D6, P < 0.05. Conclusions: CYP2D6 is the predominant enzyme responsible for the hepatic metabolism of ABT-888. Common allelic variants CYP2D6*10 and *4 are associated with significantly reduced metabolic activity towards ABT-888. CYP2D6 polymorphisms may influence the PK and therapeutic outcome of ABT-888. Its clinical relevance remains to be determined. No significant financial relationships to disclose.

A review of genetic mutation in familial Hirschsprung's disease in South Africa: towards genetic counseling

Hirschsprung's disease (HSCR) represents a complex disorder of signaling molecules, resulting from the effects of at least 9 known susceptibility genes. Affected families carry 200 times higher risk, but genetic counseling via pedigree analysis is difficult and the significance of genetic variations is unclear. This study evaluated a set of patients affected by HSCR with familial recurrence to evaluate factors of greatest value in genetic counseling. One hundred twenty patients with HSCR (including 18 kindreds) were screened for genetic variations of the 2 major susceptibility genes (RET and endothelin B receptor [EDNRB]) and compared with 60 control samples (20 per ethnic group). Familial recurrence patterns were studied for patient sex, pattern of recurrence, presence of associated syndromic features, and genetic features of major susceptibility genes. Polymerase chain reaction and HEX-SSCP analysis were performed on DBA extracted from blood/microdissected tissue samples. SSCP variants were validated and automated sequencing techniques performed on polymerase chain reaction products showing conformational variants in acrylamide gel. Familial cases had a male-female ratio of 1.5:1, male-to-male transmission (n = 10; 2 father to son), female-to-male transmissions (n = 4; 3 female carriers, female-to-female (n = 4; 2 mother to daughter), and 1 paternal RET deletion-female with very long segment aganglionosis. Increasing gene penetrance occurred in 3 pedigrees. An increased incidence of long segment HSCR was noted in families with recurrence and appeared important. No consistent mendelian trends or specific genetic sites were observed, but 3 suggested autosomal dominant and recessive in a further 3. Identified genetic variations included deletions, frame shifts, and missense mutations, as well as a number of significant single nucleotide polymorphism variations. Transmitted RET mutations occurred in 5 (30%) of 16 kindreds. Splice RET mutation plus variants of exon 17 (973L) affected 2 children with identical total colonic aganglionosis. In a 3-generation family, variations in RET exons 6, 13, and 18 (928) affected 3 male children with increasing penetration to recur as total intestinal aganglionosis in a grandchild. Mendelian transmission appears mediated by the RET proto-oncogene. EDNRB mutations suggest haplotypic gene-gene interaction. Genetic counseling remains a challenge in HSCR because of its multfactorial etiology.

Nucleotide sequence variations in the internal ribosome entry site of hepatitis C virus-1b: no association with efficacy of interferon therapy or serum HCV-RNA levels.

The extreme 5'-proximal sequences of the hepatitis C virus (HCV) genome including the 5'untranslated region (5'UTR) and the first 30 nucleotides of the core region are highly conserved, and serve as an internal ribosome entry site (IRES) that initiates the cap-independent translation of HCV polyprotein. Mutations in the IRES sequence have been shown to cause changes in the efficiency of protein translation in vitro. However, the significance of genetic variations in the IRES is not fully known in clinical settings. Pretreatment sera of 25 patients with HCV-1b infection who were treated with interferon were amplified by polymerase chain reaction (PCR), and the IRES sequence was directly sequenced. Correlation of interferon responses or other clinical features with IRES sequence variability was studied. Eleven of 25 patients were sustained responders (SR) of interferon treatment (negative serum HCV RNA and normal alanine transaminase levels for 6 months after the end of interferon treatment), and the other 14 patients were nonresponders ([NR], defined as any patient with positive serum HCV RNA within 6 months after the end of interferon therapy). In each patient, one to four nucleotide substitutions were found compared with the consensus sequence of HCV-1b genotype. There were no differences in the number of nucleotide substitutions between either SR and NR (mean, 1.8 in SR, 2.1 in NR; P = .30), and no specific variations associated with SR or NR were observed. Although NR had significantly higher serum levels of pretreatment HCV RNA than SR (median, 16 vs. <0.5 Meq/mL; P = .02), there was no correlation between the HCV-RNA level and the number of nucleotide substitutions in the IRES (mean, 1.9 nucleotide substitutions in 12 patients with HCV RNA <0.5 Meq/ mL vs. 2.1 nucleotide substitutions in 13 patients with HCV RNA >0.5 Meq/mL; P = .61). Sequence variability of the IRES has no influence on interferon efficacy or serum HCV-RNA concentrations in patients with chronic HCV-1b infection.

Nucleotide sequence variations in the internal ribosome entry site of hepatitis C virus-1b: No association with efficacy of interferon therapy or serum HCV-RNA levels

The extreme 5'-proximal sequences of the hepatitis C virus (HCV) genome including the 5'untranslated region (5'UTR) and the first 30 nucleotides of the core region are highly conserved, and serve as an internal ribosome entry site (IRES) that initiates the cap-independent translation of HCV polyprotein. Mutations in the IRES sequence have been shown to cause changes in the efficiency of protein translation in vitro. However, the significance of genetic variations in the IRES is not fully known in clinical settings. Pretreatment sera of 25 patients with HCV-1b infection who were treated with interferon were amplified by polymerase chain reaction (PCR), and the IRES sequence was directly sequenced. Correlation of interferon responses or other clinical features with IRES sequence variability was studied. Eleven of 25 patients were sustained responders (SR) of interferon treatment (negative serum HCV RNA and normal alanine transaminase levels for 6 months after the end of interferon treatment), and the other 14 patients were nonresponders ([NR], defined as any patient with positive serum HCV RNA within 6 months after the end of interferon therapy). In each patient, one to four nucleotide substitutions were found compared with the consensus sequence of HCV-1b genotype. There were no differences in the number of nucleotide substitutions between either SR and NR (mean, 1.8 in SR, 2.1 in NR; P = .30), and no specific variations associated with SR or NR were observed. Although NR had significantly higher serum levels of pretreatment HCV RNA than SR (median, 16 vs. <0.5 Meq/mL; P = .02), there was no correlation between the HCV-RNA level and the number of nucleotide substitutions in the IRES (mean, 1.9 nucleotide substitutions in 12 patients with HCV RNA <0.5 Meq/ mL vs. 2.1 nucleotide substitutions in 13 patients with HCV RNA >0.5 Meq/mL; P = .61). Sequence variability of the IRES has no influence on interferon efficacy or serum HCV-RNA concentrations in patients with chronic HCV-1b infection. (Hepatology 1997 Dec;26(6):1616-20)

Subclass distribution of salivary secretory immunoglobulin A antibodies to oral streptococci

The ability of specific secretory immunoglobulin A (S-IgA) antibodies to inhibit bacterial colonization of mucosal surfaces may be neutralized by the activity of bacterial IgA1 proteases. Because of the resistance of the IgA2 subclass to these enzymes, the biological effect of IgA1 proteases in vivo may depend on the subclass distribution of the bacterium-specific antibodies. We have estimated the subclass distribution of S-IgA antibodies in saliva samples from 13 individuals against IgA1 protease-producing (Streptococcus sanguis and Streptococcus oralis) and nonproducing (Streptococcus gordonii and Streptococcus mitis bv. 2) oral streptococci. IgA1 was found to be the predominant subclass of antibodies against these four bacteria in most of the saliva samples, corroborating previous data suggesting a role of IgA1 proteases in plaque formation. However, variation in the subclass distribution of S-IgA antibodies against the same strain was observed. In one individual, IgA2 was the predominant subclass of antibodies against all four streptococci and of total salivary S-IgA, pointing to the possible significance of genetic variations. The study also addresses methodological problems related to the quantitation of salivary antibodies by solid-phase immunoassays.

Morphologic Variants of Anopheles Albimanus and Susceptibility to Plasmodium Vivax and P. Falciparum

Three morphologically different, true-breeding phenotypes have been isolated from a strain of Anopheles albimanus from Lake Apastepeque, El Salvador. Studies with coindigenous strains of Plasmodium vivax and P. falciparum show that these phenotypes differ significantly in their susceptibility to malaria parasites. This difference is apparent both in the number of mosquitoes that become infected and the level of infection obtained. Variations in malaria susceptibility are markedly greater with P. vivax than with P. falciparum. The significance of genetic variants within a local vector population with respect to the epidemiology of malaria is discussed.