Mannose-binding lectin serum levels and (Gly54asp) gene polymorphism in recurrent aphthous stomatitis: A case-control study.

Objectives: Dysregulation of the immune response appears to play a significant role in recurrent aphthous stomatitis (RAS) development. The main objective of this case-control study is to investigate the blood levels of mannose-binding lectin (MBL) and the frequency of the MBL2 gene (gly54asp) polymorphism in RAS patients, including 40 RAS patients and 40 healthy controls. Methods: Serum MBL levels were determined by ELISA, while the PCR-restriction fragment length polymorphism was used in MBL2 genotyping. Results: The median serum MBL level was significantly lower in the RAS group than in the control group (975 ng/mL (545-1320) vs. 1760 ng/mL (1254-2134); p≤ 0.001). The MBL levels were significantly lower in the BB genotype, whereas they were significantly higher in the wild type AA with a median of 525 and 1340 ng/mL, respectively (p =0.005). The B allele was expressed in significantly higher percentages of RAS patients than in controls. There was no significant association between MBL serum levels (p=0.685) or MBL2 codon 54 genotypes (p=0.382) with the type of ulcers. Conclusion: There was an association between low MBL serum levels and the variant allele B of the MBL2 (gly54asp) gene, and the susceptibility to RAS. As a result, potential novel therapeutic options for RAS patients with MBL deficiency should be investigated.

The cost-effectiveness of genotyping versus sequencing for prenatal cystic fibrosis carrier screening.

OBJECTIVE: We investigated the cost-effectiveness of three sequential prenatal cystic fibrosis (CF) carrier screening strategies: genotyping both partners, genotyping one partner then sequencing the second, and sequencing both partners. METHOD: A decision-analytic model compared the strategies in a theoretical cohort of four million pregnant couples in the US population and five racial/ethnic sub-populations. Inputs were obtained from literature and varied in sensitivity analysis. Outcomes included cost per quality-adjusted life year (QALY), missed carrier couples, affected newborns, missed prenatal diagnoses, terminations, and procedure-related losses. The cost-effectiveness threshold was $100,000/QALY. RESULTS: Sequencing both partners identified 1099 carrier couples that were missed by genotyping both partners, leading to 273 fewer missed prenatal diagnoses, 152 more terminations, and 152 fewer affected newborns. A similar trend was observed in the genotyping followed by sequencing strategy. The incremental cost-effectiveness ratio of genotyping followed by sequencing compared to genotyping both partners was $180,004/QALY and the incremental cost-effectiveness ratio of sequencing both partners compared to genotyping followed by sequencing was $17.6 million/QALY. Sequencing both partners was cost-effective below $339 per test, genotyping/sequencing between $340 and $1837, and genotyping both partners above $1838. Sequencing was not cost-effective among five racial/ethnic sub-populations. CONCLUSION: Despite improved outcomes, sequencing for prenatal CF carrier screening was not cost-effective compared to genotyping. The clinical significance of the incremental cost-effectiveness of CF carrier screening is a matter of deliberation for public policy debate.

HBV Genotype: A Significant Risk Factor in Determining Which Patients With Chronic HBV Infection Should Undergo Surveillance for HCC: The Hepatitis B Alaska Study.

BACKGROUND AND AIMS: Information is limited regarding HBV genotype and the outcome of chronic HBV (CHB) infection. We examined the effect of HBV genotype on HCC occurrence in Alaska Native (AN) persons with CHB, where five HBV genotypes are found: A2, B6, C2, D, and F1. APPROACH AND RESULTS: We calculated HCC incidence per 1,000 person-years of follow-up to determine which groups by age, sex, and genotype met current American Association for the Study of Liver Diseases (AASLD) HCC surveillance criteria. We used Poisson regression to compare HCC risk by genotype, age, sex, and Alaska region. Incidence of HCC was calculated using the sex-specific AASLD cutoff recommended for the Asian population of 50 years for women and 40 years for men. HCC screening was conducted semiannually using alpha-fetoprotein levels and abdominal ultrasound. Among 1,185 AN persons, median follow-up was 35.1 years; 667 (63%) were male. The HBV genotype distribution was 49% D, 18% F, 13% A, 6% C, 3% B, 0.1% H, and 12% undetermined. Sixty-three cases of HCC occurred. HCC incidence for genotype F was 5.73 per 1,000 person-years of follow-up, followed by 4.77 for C, 1.28 for A, 0.47 for D, and 0.00 for B. The HCC risk was higher for genotypes F (relative rate [RR], 12.7; 95% CI, 6.1-26.4), C (RR, 10.6; 95% CI, 4.3-26.0), and A (RR, 2.9; 95% CI, 1.0-8.0) compared to genotypes B and D. Among men < 40 years of age and women < 50 years of age, genotype F had the highest incidence (4.79/1,000 person-years). CONCLUSIONS: HBV genotype was strongly associated with HCC. HBV genotype should be considered in risk factor stratification.

Estimating heritability and its enrichment in tissue-specific gene sets in admixed populations.

It is important to study the genetics of complex traits in diverse populations. Here, we introduce covariate-adjusted linkage disequilibrium (LD) score regression (cov-LDSC), a method to estimate SNP-heritability (${\boldsymbol{h}}_{\boldsymbol{g}}^{\mathbf{2}})$ and its enrichment in homogenous and admixed populations with summary statistics and in-sample LD estimates. In-sample LD can be estimated from a subset of the genome-wide association studies samples, allowing our method to be applied efficiently to very large cohorts. In simulations, we show that unadjusted LDSC underestimates ${\boldsymbol{h}}_{\boldsymbol{g}}^{\mathbf{2}}$ by 10-60% in admixed populations; in contrast, cov-LDSC is robustly accurate. We apply cov-LDSC to genotyping data from 8124 individuals, mostly of admixed ancestry, from the Slim Initiative in Genomic Medicine for the Americas study, and to approximately 161 000 Latino-ancestry individuals, 47 000 African American-ancestry individuals and 135 000 European-ancestry individuals, as classified by 23andMe. We estimate ${\boldsymbol{h}}_{\boldsymbol{g}}^{\mathbf{2}}$ and detect heritability enrichment in three quantitative and five dichotomous phenotypes, making this, to our knowledge, the most comprehensive heritability-based analysis of admixed individuals to date. Most traits have high concordance of ${\boldsymbol{h}}_{\boldsymbol{g}}^{\mathbf{2}}$ and consistent tissue-specific heritability enrichment among different populations. However, for age at menarche, we observe population-specific heritability estimates of ${\boldsymbol{h}}_{\boldsymbol{g}}^{\mathbf{2}}$. We observe consistent patterns of tissue-specific heritability enrichment across populations; for example, in the limbic system for BMI, the per-standardized-annotation effect size $ \tau $* is 0.16 ± 0.04, 0.28 ± 0.11 and 0.18 ± 0.03 in the Latino-, African American- and European-ancestry populations, respectively. Our approach is a powerful way to analyze genetic data for complex traits from admixed populations.

Cenário epidemiológico da Covid-19 no estado do Rio de Janeiro Período de Análise: março/2020 a abril/2021 / Epidemiological scenario from Covid-19 in the state of Rio de Janeiro Analysis Period: March/2020 to April/2021

O Estado do Rio de Janeiro vem monitorando a evolução das variantes da Covid-19 por meio de três processos de seleção de amostras. O primeiro é o monitoramento realizado pelos municípios que notifica e solicita o sequenciamento, seguindo os critérios e fluxos descritos na Nota técnica da SES-RJ Nº 09/2021. O segundo faz parte da Vigilância Genômica organizada pelo Ministério da Saúde, onde três amostras aleatórias são enviadas pelo Lacen/RJ para FUNED/MG, de acordo com os critérios estabelecidos pela SVS/ FUNED. O terceiro é através de um estudo com financiamento da Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) que iniciou em março de 2021 e irá realizar a genotipagem de um total de 4.800 amostras nos próximos seis meses, sendo 400 a cada 15 dias. Por fim, a Secretaria de Estado de Saúde tem envidado esforços em ações de redução de risco, como a vacinação, ampliação de testagem, monitoramento genômico e promoção de saúde em todo o estado do Rio de Janeiro. E é recomendado manter as medidas de proteção à vida: como evitar aglomeração, usar de máscara, lavar as mãos e fazer higienização das mãos com álcool 70°.

RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID.

Inference of relationships from whole-genome genetic data of a cohort is a crucial prerequisite for genome-wide association studies. Typically, relationships are inferred by computing the kinship coefficients (ϕ) and the genome-wide probability of zero IBD sharing (π0) among all pairs of individuals. Current leading methods are based on pairwise comparisons, which may not scale up to very large cohorts (e.g., sample size >1 million). Here, we propose an efficient relationship inference method, RAFFI. RAFFI leverages the efficient RaPID method to call IBD segments first, then estimate the ϕ and π0 from detected IBD segments. This inference is achieved by a data-driven approach that adjusts the estimation based on phasing quality and genotyping quality. Using simulations, we showed that RAFFI is robust against phasing/genotyping errors, admix events, and varying marker densities, and achieves higher accuracy compared to KING, the current leading method, especially for more distant relatives. When applied to the phased UK Biobank data with ~500K individuals, RAFFI is approximately 18 times faster than KING. We expect RAFFI will offer fast and accurate relatedness inference for even larger cohorts.

Marker genotyping error effects on genomic predictions under different genetic architectures.

This study aimed to determine the effect of different rates of marker genotyping error on the accuracy of genomic prediction that was examined under distinct marker and quantitative trait loci (QTL) densities and different heritability estimates using a stochastic simulation approach. For each scenario of simulation, a reference population with phenotypic and genotypic records and a validation population with only genotypic records were considered. Marker effects were estimated in the reference population, and then their genotypic records were used to predict genomic breeding values in the validation population. The prediction accuracy was calculated as the correlation between estimated and true breeding values. The prediction bias was examined by computing the regression of true genomic breeding value on estimated genomic breeding value. The accuracy of the genomic evaluation was the highest in a scenario with no marker genotyping error and varied from 0.731 to 0.934. The accuracy of the genomic evaluation was the lowest in a scenario with marker genotyping error equal to 20% and changed from 0.517 to 0.762. The unbiased regression coefficients of true genomic breeding value on estimated genomic breeding value were obtained in the reference and validation populations when the rate of marker genotyping error was equal to zero. The results showed that marker genotyping error can reduce the accuracy of genomic evaluations. Moreover, marker genotyping error can provide biased estimates of genomic breeding values. Therefore, for obtaining accurate results it is recommended to minimize the marker genotyping errors to zero in genomic evaluation programs.

coPLINK: A complementary tool to PLINK.

In genome-wide association studies (GWAS), a wide variety of analysis tools have been designed, leading to various formats of GWAS data. How to convert a dataset in non-PLINK format into PLINK format to use its powerful analysis performance, or to convert a dataset in PLINK format into the format of other analysis tools, is a problem that needs to be faced and solved. To address this issue, we developed a tool called coPLINK, a complementary tool to PLINK, to cooperate with PLINK to implement the conversions of GWAS data formats and to provide some additional functions, such as data files comparison. The tool can implement mutual conversions not only between an existing data format and PLINK PED/BED, but also between a user-defined data format and PLINK PED. The usage and performance of the tool are similar to PLINK. The characteristics of the conversions of existing data formats and user-defined formats make it be a good assistant to PLINK or other tools and, have good potential for GWAS studies or other works.

Outcomes of prior cervical cytology and HR-HPV testing in women subsequently diagnosed with CIN1, CIN2/3, and invasive cervical cancer: a 4-year routine clinical experience after implementation of systematic training and quality control programs.

BACKGROUND: In 2013, Jinan KingMed Diagnostics (JKD) first established a systematic cervical cytology training and quality control (QC) program in Shandong Province, China. We compared the efficacy of high-risk human papillomavirus (HR-HPV) detection, cytology, and their combination in routine clinical practice after the implementation of the training and QC program to identify the optimal first-line screening method in this region. METHODS: The data of patients histologically diagnosed with cervical intraepithelial neoplasia (CIN) 1, CIN2/3, and invasive cervical cancer (ICC) between January 2014 and December 2017 were retrieved from the JKD database. Cytology and/or HR-HPV testing results within 3 months preceding the CIN1 diagnoses and 6 months preceding the CIN2/3 and ICC diagnoses were analyzed. RESULTS: Prior screening data were available for 1829 CIN1 patients, 2309 CIN2/3 patients, and 680 ICC patients. Cytology alone and HR-HPV testing alone had similar rates of positive results for CIN2/3 (97.2% [854/879] vs. 95.4% [864/906], P = 0.105) and ICC detection (89.1% [205/230] vs. 92.7% [204/220], P = 0.185). Compared with either method alone, co-testing slightly increased the screening sensitivity for CIN2/3 (99.8% [523/524], all P < 0.001) and ICC (99.6% [229/230], all P < 0.001) detection. In the CIN1 group, cervical cytology alone (92.9% [520/560]) was more sensitive than HR-HPV testing alone (79.9% [570/713], P < 0.001), and co-testing (95.3% [530/556]) did not significantly improve the screening sensitivity (P = 0.105). CONCLUSIONS: After the implementation of a systematic training and QC program, both cytology and HR-HPV testing may be adopted for primary cervical cancer screening in Shandong Province.

Noninvasive Fetal Genotyping by Droplet Digital PCR to Identify Maternally Inherited Monogenic Diabetes Variants.

BACKGROUND: Babies of women with heterozygous pathogenic glucokinase (GCK) variants causing mild fasting hyperglycemia are at risk of macrosomia if they do not inherit the variant. Conversely, babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A) diabetes variant are at increased risk of high birth weight. Noninvasive fetal genotyping for maternal pathogenic variants would inform pregnancy management. METHODS: Droplet digital PCR was used to quantify reference and variant alleles in cell-free DNA extracted from blood from 38 pregnant women heterozygous for a GCK or HNF4A variant and to determine fetal fraction by measurement of informative maternal and paternal variants. Droplet numbers positive for the reference/alternate allele together with the fetal fraction were used in a Bayesian analysis to derive probability for the fetal genotype. The babies' genotypes were ascertained postnatally by Sanger sequencing. RESULTS: Droplet digital PCR assays for GCK or HNF4A variants were validated for testing in all 38 pregnancies. Fetal fraction of ≥2% was demonstrated in at least 1 cell-free DNA sample from 33 pregnancies. A threshold of ≥0.95 for calling homozygous reference genotypes and ≤0.05 for heterozygous fetal genotypes allowed correct genotype calls for all 33 pregnancies with no false-positive results. In 30 of 33 pregnancies, a result was obtained from a single blood sample. CONCLUSIONS: This assay can be used to identify pregnancies at risk of macrosomia due to maternal monogenic diabetes variants.

Inter- and Intrafamilial Phenotypic Variability in Individuals with Collagen-Related Osteogenesis Imperfecta.

Osteogenesis imperfecta (OI) is a rare genetic disorder also known as a "brittle bone disease." Around 90% of patients with OI harbor loss-of-function or dominant negative pathogenic variants in the COL1A1 and COL1A2 genes, which code for collagen type I α1 and α2 chains. Collagen-related forms of the disorder are classified as Sillence OI types I-IV. OI phenotype expression ranges from mild to lethal. The current study aims to evaluate associations between interfamilial and intrafamilial phenotypic variability and genotype characteristics of patients with collagen-related OI. The study was based on a systematic review of collagen-related OI cases from the University of Tartu OI database (n = 137 individuals from 81 families) and the Dalgleish database (n = 479 individuals). Interfamilial variability analysis has shown that 17.74% of all studied OI-related variants were associated with the same phenotype. The remaining 82.26% of pathogenic variants were associated with variable phenotypes. Additionally, higher interfamilial variability correlated with the COL1A1 gene (P value = 0.001) and dominant-negative variants (P value = 0.0007). Within intrafamilial variability, 32.81% families had increasing or decreasing OI phenotype severity across generations. Higher intrafamilial variability of phenotypes correlated with the collagen I dominant negative variants (P value = 0.0246). The current study shows that, in line with other phenotype modification factors, OI interfamilial and intrafamilial diversity potential is associated with the genotype characteristics of the OI-causing pathogenic variants. The results of the current study may advance knowledge of OI phenotype modification as well as assist family planning and the evaluation of disease progression in subsequent generations.

Performance of pedigree and various forms of marker-derived relationship coefficients in genomic prediction and their correlations.

In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix (A) and three types of marker-based relationship matrices ( G ) including two identical by descent, that is G K and G M and one identical by state, G V as well as four Gaussian kernel ( GK ) similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as K = λ G + 1 - λ A , where the weight ( λ ) assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK-based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK-based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or A kinship matrices or any of the linear combinations.

Donor PNPLA3 and TM6SF2 Variant Alleles Confer Additive Risks for Graft Steatosis After Liver Transplantation.

BACKGROUND: The rs58542926 polymorphism in transmembrane 6 superfamily member 2 (TM6SF2) is a genetic factor predisposing to nonalcoholic fatty liver disease. We aimed to explore the effect of recipient and donor TM6SF2 rs58542926 genotypes on liver graft fat content after liver transplantation. METHODS: Steatosis was evaluated in liver biopsies from 268 adult recipients. The influence of recipient and donor TM6SF2 genotypes, patatin-like phospholipase domain-containing 3 (PNPLA3) rs738409 genotypes, and nongenetic factors on the steatosis grade assessed 6-30 months after transplantation was analyzed by ordinal logistic regression. RESULTS: The presence of the TM6SF2 c.499A allele in the donor (P = 0.014), PNPLA3 c.444G allele in the donor (P < 0.001), posttransplant body mass index (P < 0.001), and serum triglycerides (P = 0.047) independently predicted increased liver fat content on multivariable analysis, whereas noncirrhotic liver disease, as an indication for liver transplantation, was associated with lower risk of steatosis (P = 0.003). The effects of the donor TM6SF2 A and PNPLA3 G alleles were additive, with an odds ratio of 4.90 (95% confidence interval, 2.01-13.00; P < 0.001), when both minor alleles were present compared with an odds ratio of 2.22 (95% confidence interval, 1.42-3.61; P = 0.002) when only one of these alleles was present. CONCLUSIONS: The donor TM6SF2 c.499A allele is an independent risk factor of liver graft steatosis after liver transplantation that is additive to the effects of donor PNPLA3 c.444G allele.

Performance of HPV Genotyping Combined with p16/Ki-67 in Detection of Cervical Precancer and Cancer Among HPV-Positive Chinese Women.

Women with positive high-risk human papillomavirus (hrHPV) need efficient triage testing to determine colposcopy referrals. Triage strategies of combining p16/Ki-67 with extended HPV genotyping were evaluated in this study. In total, 899 women attending cervical cancer screening program and 858 women referred to colposcopy from five hospitals were recruited. All the participants were tested by HPV assays and p16/Ki-67 dual staining. Colposcopy and biopsy were performed on women with any abnormal results. HPV genotypes were divided into four strata (HPV16/18, HPV31/33/58/52, HPV45/59/56/66, and HPV51/39/68/35) according to their risks for cervical intraepithelial neoplasia grade 3 or worse (CIN3+). The positive rates of four genotype strata among CIN3+ women were 3.47% (HPV51/39/68/35), 7.73% (HPV45/59/56/66), 14.7% (HPV31/33/58/52), and 78.1% (HPV16/18), respectively (P trend < 0.001). The positive rates of p16/Ki-67 increased with the elevation of HPV risk hierarchical from 65.0% in HPV51/39/68/35-positive women to 88.0% in HPV16/18-positive women (P trend < 0.001). p16/Ki-67 was an effective method for risk stratification of CIN2+ among HPV31/33/58/52- and HPV45/59/56/66-positive women [HPV31/33/58/52: OR for dual stain+ (ORDS+) of 26.7 (16.8-42.4) and OR for dual stain- (ORDS-) of 3.87(1.89-7.91); HPV45/59/56/66: ORDS+ of 10.3(5.05-21.0) and ORDS- of 1.27(0.38-4.26)]. The combination of HPV16/18 genotyping and p16/Ki-67 triage of HPV31/33/58/52/45/59/56/66-positive women resulted in a lower referral rate (40.1% vs. 41.3%; P < 0.001) as compared with triage of 12 other HPV-positive women with p16/Ki-67, although sensitivity and specificity levels for these two strategies were identical. Combining HPV extended genotyping and p16/Ki-67 can be considered as a promising strategy for cervical cancer screening and triage.

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.

Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.

Prevalence of HPV-16/18 genotypes and immediate histopathologic correlation results in a Chinese population with negative cytology and positive high-risk HPV testing.

BACKGROUND: The objective of this study was to examine the prevalence of human papillomavirus 16/18 (HPV-16/18) genotypes and immediate histopathologic correlations in a Chinese population with negative cytology and positive high-risk human papillomavirus (hrHPV) testing. METHODS: Patients who had documented negative cytology with immediate follow-up (within the 6 months after negative for intraepithelial lesion or malignancy Papanicolaou [Pap] testing), including a histopathologic examination and/or hrHPV testing, between 2011 and 2018 were included, and the data were analyzed. RESULTS: Among 1,424,182 Pap tests, 1,333,453 (93.6%) were interpreted as negative cytology. Although conventional Pap smears had the highest reporting rate, cervical intraepithelial neoplasia 2 and higher (CIN-2+) lesions were detected significantly more with liquid-based cytology preparations (2.1%) than the conventional method (1.4%; P < .01). The overall hrHPV-positive rate was 14.9% (25,507 of 171,273) in the women with negative cytology. Among the 18,423 cytology-negative, HPV-positive cases tested with the Cobas assay, the overall HPV-16/18 prevalence was 24.7%, with 17.9% being HPV-16-positive, 6.2% being HPV-18-positive, and 0.6% being positive for both HPV-16 and HPV-18. The immediate histopathologic examination was documented for 21,796 women with cotesting results, including 8915 HPV-positive cases and 12,881 HPV-negative cases. CIN-2+ lesions were diagnosed in 15.2% of the HPV-16-positive cases; this rate was significantly higher than the rates seen in the HPV-18-positive cases (4.8%) and the cases positive for 1 of the other 12 types of HPV (3.0%). CONCLUSIONS: This is by far the largest routine clinical practice report of HPV-16/18 genotyping and histopathologic examination in negative-cytology women and the first report of such an investigation in the Chinese population. This study indicates enhanced risk stratification with HPV-16/18 genotype testing in HPV-positive, cytology-negative women in the Chinese population.

Human Papillomavirus Genotyping Compared With a Qualitative High-Risk Human Papillomavirus Test After Treatment of High-Grade Cervical Intraepithelial Neoplasia: A Systematic Review.

OBJECTIVE: To systematically examine human papillomavirus (HPV) genotyping compared with qualitative high-risk HPV result during follow-up after treatment of high-grade cervical intraepithelial neoplasia (CIN), for risk estimation of posttreatment high-grade CIN. DATA SOURCES: MEDLINE, Cochrane, and ClinicalTrials.gov were searched from January 2000 to April 2019 for prospective studies of women and retrospective studies of residual specimens from women, tested using HPV assays with genotype reporting. METHODS OF STUDY SELECTION: The primary outcome was posttreatment high-grade CIN after treatment of high-grade CIN. Risk of bias (individual study quality) was evaluated with a modified Newcastle-Ottawa Scale. Overall quality of evidence for the risk estimate outcomes was evaluated using modified GRADE methodology for observational diagnostic studies. TABULATION, INTEGRATION, AND RESULTS: Of the 233 identified abstracts, 33 full-text articles were retrieved, and seven studies were included in the synthesis. The risk of bias was deemed to be low. Either a positive qualitative HPV test result or a positive test result for the same genotype that was present pretreatment have a sensitivity for predicting posttreatment high-grade CIN that approaches 100%. However, the positive predictive value (PPV) for the same genotype result pretreatment and posttreatment (median 44.4%) is about double the PPV (median 22.2%) for qualitative HPV results. The PPV of a new HPV infection posttreatment approximates zero. Human papillomavirus genotyping discriminated risk of posttreatment high-grade CIN to a clinically significant degree for women after treatment procedures for high-grade CIN lesions, when same-genotype persistence was compared with new genotype infection. CONCLUSION: There is moderately high-quality evidence to support the improved clinical utility of HPV genotyping compared with qualitative HPV positivity to follow-up after treatment of high-grade CIN. SYSTEMATIC REVIEW REGISTRATION: PROSPERO: CRD42018091095. FUNDING SOURCE: Becton, Dickinson and Company, BD Life Sciences-Diagnostic Systems.

The impact of liver transplant recipient and donor genetic variability on tacrolimus exposure and transplant outcome.

This study investigated the effect of recipient and donor genetic variability on dose-adjusted steady-state tacrolimus concentrations (Css ) and clinical outcomes 3 and 6 months after liver transplant. Twenty-nine recipients and matched donor blood samples were genotyped for 27 single nucleotide polymorphisms including CYP3A5*3 (rs776746), ABCB1 haplotype and immune genes. Associations between genetic variability and clinical parameters and Css and the occurrence of rejection and nephrotoxicity were analysed by multivariate and multinomial logistic regression modelling and Jonckheere-Terpstra tests examined the impact of combined donor/recipient CYP3A5 expression on Css . At 3 months post-transplant modelling revealed an association between tacrolimus Css and recipient CASP1 rs580523 genotype (P = 0.005), accounting for 52% Css variance. Jonckheere-Terpstra tests revealed that as combined donor/recipient CYP3A5 expression increased, Css decreased (P = 0.010 [3 months], 0.018 [6 months]). As this is the first report of CASP1 genetic variability influencing tacrolimus Css , further validation in larger cohorts is required.

Impact of somatic molecular profiling on clinical trial outcomes in rare epithelial gynecologic cancer patients.

OBJECTIVES: Conducting clinical trials in rare malignancies is challenging due to the limited number of patients and differences in biologic behavior. We investigated the feasibility and clinical utility of using genomic profiling for rare gynecologic malignancies. METHODS: Rare epithelial gynecologic cancer patients were analyzed for somatic variants through an institutional molecular profiling program using the Sequenom MassArray platform or the TruSeq Amplicon Cancer Panel on the MiSeq platform. Clinical trial outcomes by RECIST 1.1, and time on treatment were evaluated. RESULTS: From March 2012 to November 2015, 767 gynecologic patients were enrolled and 194 (27%) were classified as rare epithelial malignancies. At least one somatic mutation was identified in 72% of patients, most commonly in TP53 (39%), KRAS (28%) and PIK3CA (27%). A total of 14% of patients were treated on genotype-matched trials. There were no significant differences in overall response rate between genotype-matched versus unmatched trials, nor in median time on treatment between genotype trials and the immediate prior systemic standard treatment. Among 13 evaluable Low Grade Serous ovarian cancer patients treated on genotype-matched trials with MEK inhibitor-based targeted combinations, there were four partial responses. CONCLUSIONS: Somatic molecular profiling is feasible and enables the identification of patients with rare gynecologic cancers who are candidates for genotype-matched clinical trials. Genotype-matched trials, predominantly MEK-based combinations in KRAS and/or NRAS mutant Low Grade Serous ovarian cancer patients, and genotype-unmatched trials, have shown potential clinical activity. Prospective trials with integrated genotyping are warranted to assess the clinical utility of next generation sequencing tests as a standard clinical application in rare malignancies.

Analyzing the clinical actionability of germline pharmacogenomic findings in oncology.

BACKGROUND: Germline and tumor pharmacogenomics impact drug responses, but germline markers less commonly guide oncology prescribing. The authors hypothesized that a critical number of clinically actionable germline pharmacogenomic associations exist, representing clinical implementation opportunities. METHODS: In total, 125 oncology drugs were analyzed for positive germline pharmacogenomic associations in journals with impact factors ≥5. Studies were assessed for design and genotyping quality, clinically relevant outcomes, statistical rigor, and evidence of drug-gene effects. Associations from studies of high methodologic quality were deemed potentially clinically actionable, and translational summaries were written as point-of-care clinical decision support (CDS) tools and formally evaluated using the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument. RESULTS: The authors identified germline pharmacogenomic results for 56 of 125 oncology drugs (45%) across 173 publications. Actionable associations were detected for 12 drugs, including 6 that had germline pharmacogenomic information within US Food and Drug Administration labels or published guidelines (capecitabine/fluorouracil/dihydropyrimidine dehydrogenase [DPYD], irinotecan/uridine diphosphate glucuronosyltransferase family 1 member A1 [UGT1A1], mercaptopurine/thioguanine/thiopurine S-methyltransferase [TPMT], tamoxifen/cytochrome P450 [CYP] family 2 subfamily D member 6 [CYP2D6]), and 6 others were novel (asparaginase/nuclear factor of activated T-cells 2 [NFATC2]/human leukocyte antigen D-related ß1 [HLA-DRB1], cisplatin/acylphosphatase 2 [ACYP2], doxorubicin/adenosine triphosphate-binding cassette subfamily C member 2/Rac family small guanosine triphosphatase 2/neutrophil cytosolic factor 4 [ABCC2/RAC2/NCF4], lapatinib/human leukocyte antigen DQ α1 [HLA-DQA1], sunitinib/cytochrome P450 family 3 subfamily A member 5 [CYP3A5], vincristine/centrosomal protein 72 [CEP72]). By using AGREE II, the developed CDS summaries had high mean ± standard deviation scores (maximum score, 100) for scope and purpose (92.7 ± 5.1) and rigour of development (87.6 ± 7.4) and moderate yet robust scores for clarity of presentation (58.6 ± 25.1) and applicability (55.9 ± 24.6). The overall mean guideline quality score was 5.2 ± 1.0 (maximum score, 7). Germline pharmacogenomic CDS summaries for these 12 drugs were recommended for implementation. CONCLUSIONS: Several oncology drugs have actionable germline pharmacogenomic information, justifying their delivery through institutional pharmacogenomic implementations to determine clinical utility. Cancer 2018;124:3052-65. © 2018 American Cancer Society.