Interpreting variants in genes affected by clonal hematopoiesis in population data

Reference population databases like the Genome Aggregation Database (gnomAD) have improved our ability to interpret the human genome. Variant frequencies and frequency-derived tools (such as depletion scores) have become fundamental to variant interpretation and the assessment of variant-gene-disease relationships. Clonal hematopoiesis (CH) obstructs variant interpretation as somatic variants that provide proliferative advantage will affect variant frequencies, depletion scores, and downstream filtering. Further, default filtering of variants or genes associated with CH risks filtering bona fide germline variants as variants associated with CH can also cause Mendelian conditions. Here, we provide our insights on interpreting population variant data in genes affected by clonal hematopoiesis, as well as recommendations for careful review of 36 established CH genes associated with neurodevelopmental conditions.

Associations between hyperthyroidism and adverse obstetric and neonatal outcomes: A study of a population database including almost 17,000 women with hyperthyroidism

OBJECTIVE

Large population-based studies on maternal hyperthyroidism's effect on antepartum, intrapartum, and neonatal complications are few. Most of these studies were small or did not evaluate a broad scope of possible complications. Therefore, a large population-based cohort study was conducted to study the associations between maternal hyperthyroidism and pregnancy and perinatal complications.

DESIGN

This is a retrospective population-based cohort study utilizing data from the Healthcare Cost and Utilization Project-Nationwide Inpatient Sample over 11 years from 2004 to 2014.

PATIENTS

16,984 deliveries to women with hyperthyroidism and 9,079,804 deliveries to mothers who did not suffer of hyperthyroidism.

METHODS

A cohort of all deliveries between 2004 and 2014 inclusively was created. Within this group, all deliveries to women with hyperthyroidism were the study group (n = 16,984) and the remaining deliveries were categorized as nonhyperthyroidism births and comprised the reference group (n = 9,079,804). The main outcome measures were pregnancy and perinatal complications.

RESULTS

Maternal hyperthyroidism was associated with several pregnancy and perinatal complications, including increased risks of gestational hypertension (adjusted odds ratio [aOR]: 1.236, 95% confidence interval [CI]: 1.045-1.462, p = .013) and preeclampsia (aOR: 1.190, 95% CI: 1.006-1.408, p = .042). These patients are more likely to experience preterm premature rupture of membranes (aOR: 1.322, 95% CI: 1.007-1.735, p = .044), preterm delivery (aOR: 1.287 95% CI: 1.132-1.465, p < .001), placental previa (aOR: 1.527, 95% CI: 1.082-2.155, p = .016), and suffer from venous thromboembolism (aOR: 2.894, 95% CI: 1.293-6.475, p = .010). As for neonatal outcomes, small for gestational age and stillbirth were more likely to occur in the offspring of women with hyperthyroidism (aOR: 1.688, 95% CI: 1.437-1.984, p < .001 and aOR: 1.647, 95% CI: 1.109-2.447, p = .013, respectively).

CONCLUSIONS

Women with hyperthyroidism are more likely to experience pregnancy, delivery, and neonatal complications. We found an association between hyperthyroidism and hypertensive disorders, preterm delivery, and intrauterine fetal death.

Incidence and Risk Factors for New-Onset Diabetes Mellitus After Surgical Resection of Pancreatic Cystic Lesions: A MarketScan Study

OBJECTIVES

There is a paucity of literature evaluating new-onset diabetes mellitus (NODM) after resection of pancreatic cystic lesions (PCLs). We sought to characterize the incidence and risk factors associated with NODM after partial pancreatectomy for PCLs.

METHODS

We utilized the IBM MarketScan Database (2012-2018) to identify all nondiabetic adults who underwent partial pancreatectomy for PCLs. Patients with any other pancreatic disease were excluded. We performed Kaplan-Meier analysis and multivariable Cox proportional hazards regression to define the incidence and risk factors of postoperative NODM.

RESULTS

Among 311 patients, the overall risk (95% confidence interval) of NODM was 9.1% (6.3-12.9%), 15.1% (11.3-20.2%), and 20.2% (15.3-26.4%) at 6, 12 and 24 months, respectively. Multivariable analysis (adjusted hazard ratio; 95% confidence interval) revealed that older age (1.97; 1.04-3.72; 55-64 vs 18-54 years), obesity (2.63; 1.35-5.12), hypertension (1.79; 1.01-3.17), and cardiovascular disease (2.54; 1.02-6.28) were independent predictors of NODM. Rates of NODM were similar after distal pancreatectomy versus pancreaticoduodenectomy.

CONCLUSIONS

Within 2 years, 1 in 5 patients without any other pancreatic disease will develop NODM after partial pancreatectomy for PCLs. Those with advanced age, metabolic syndrome features, and/or cardiovascular disease may benefit from preoperative counseling and intensive postoperative monitoring, education, and treatment for diabetes mellitus.

Analysis of Worldwide Carrier Frequency and Predicted Genetic Prevalence of Autosomal Recessive Congenital Hypothyroidism Based on a General Population Database

To assess how genomic information of the general population reflects probabilities of developing diseases and the differences in those probabilities among ethnic groups, a general population database was analyzed with an example of congenital hypothyroidism. Twelve candidate genes that follow an autosomal recessive inheritance pattern in congenital hypothyroidism (SLC5A5, TPO, TG, IYD, DUOXA2, DUOX2, TSHR, SLC26A7, GLIS3, FOXE1, TSHB, TRHR) in the gnomAD database (v2.1.1) were analyzed. The carrier frequency (CF) and predicted genetic prevalence (pGP) were estimated. The total CF in the overall population was 3.6%. DUOX2 showed the highest CF (1.8%), followed by TG (0.46%), TPO (0.44%), TSHR (0.31%), SLC26A7 (0.144%), DUOXA2 (0.141%), IYD (0.08%), SLC5A5 (0.06%), TRHR (0.059%), GLIS3 (0.059%), TSHB (0.04%), and FOXE1 (0%). The pGP in the overall population was 10.01 individuals per 100,000 births (1:9992). The highest pGP was in the East Asian population at 52.48 per 100,000 births (1:1905), followed by Finnish (35.96), Non-Finnish European (9.56), African/African American (4.0), Latino/Admixed American (3.89), South Asian (3.56), and Ashkenazi Jewish (1.81) groups. Comparing the pGP with the real incidence of congenital hypothyroidism, the pGP in East Asian populations was highly consistent with the real incidence.

Phenome-wide Burden of Copy-Number Variation in the UK Biobank

Copy-number variations (CNVs) represent a significant proportion of the genetic differences between individuals and many CNVs associate causally with syndromic disease and clinical outcomes. Here, we characterize the landscape of copy-number variation and their phenome-wide effects in a sample of 472,228 array-genotyped individuals from the UK Biobank. In addition to population-level selection effects against genic loci conferring high mortality, we describe genetic burden from potentially pathogenic and previously uncharacterized CNV loci across more than 3,000 quantitative and dichotomous traits, with separate analyses for common and rare classes of variation. Specifically, we highlight the effects of CNVs at two well-known syndromic loci 16p11.2 and 22q11.2, previously uncharacterized variation at 9p23, and several genic associations in the context of acute coronary artery disease and high body mass index. Our data constitute a deeply contextualized portrait of population-wide burden of copy-number variation, as well as a series of dosage-mediated genic associations across the medical phenome.

Will cesarean section increase the risk of interstitial cystitis/painful bladder syndrome?

AIMS

A high number of patients with interstitial cystitis/painful bladder syndrome (IC/PBS) have a history of pelvic surgeries, and cesarean section is one of the most common pelvic surgeries in women. This study aimed to investigate if cesarean section increases the risk of IC/PBS.

METHODS

Women who exclusively gave birth through cesarean section or vaginal delivery were identified from a nationwide database between 2002 and 2013. All were followed up during the study period to detect the event of IC/PBS. The IC/PBS hazard ratio (HR) in the cesarean cohort was compared with the vaginal delivery cohort with and without matching for confounding factors.

RESULTS

The unmatched group included 22 158 cesarean deliveries and 40 214 vaginal deliveries. The IC/PBS HR in the cesarean cohort compared with that in the vaginal delivery cohort was 1.370 (95% confidence interval [CI], 0.903-2.079; P = 0.139). In the matched group, 8368 women were matched in each cesarean and vaginal delivery cohort using propensity scores for age and comorbidities. The IC/PBS HR was 0.725 (95%CI, 0.358-1.471; P = 0.373). Both HRs in these two groups were not significantly different. The incidence density of IC/PBS in delivered women, non-delivery women, and the general female population were not significantly different either (0.310, 0.255, and 0.292 per 1000 person-years, respectively; P = 0.549).

CONCLUSIONS

The risk of IC/PBS was not different between cesarean and vaginal delivery after controlling the confounding factors in this cohort study. Cesarean section has no causal effect on IC/BPS. Furthermore, delivery was not a risk factor for IC/PBS.

Deep genealogical analysis of a large cohort of participants in the CARTaGENE project (Quebec, Canada)

BACKGROUND

Genealogical analysis helps to better understand the genetic structure of populations. The population of Quebec (Canada) often serves as a model for this type of analysis, having one of the world's most complete genealogical databases.

AIM

The main objective of this study was to reconstruct, analyse and compare the ascending genealogies of participants to CARTaGENE, a project that aims at building a database on various aspects of public health.

SUBJECTS AND METHODS

In total, 5110 genealogies from four Quebec regions were reconstructed. Distribution of ancestors, completeness and depth of the genealogies, characteristics of immigrant ancestors and kinship and inbreeding coefficients were analysed.

RESULTS

Most genealogies go back to the 17th century, with a mean genealogical depth of 10 generations. Origins of immigrant ancestors are more diverse in the Montreal region, resulting in lower inbreeding and kinship among the participants from this region. Inbreeding and kinship values are mainly explained by remote genealogical links (from 6 to 11 generations).

CONCLUSION

Deep genealogies allowed for a precise measurement of the geographic origins of the participants' immigrant ancestors, as well as inbreeding and kinship ties in the population, which may be crucial for studies aiming to identify genetic variations associated with Mendelian or complex diseases.

Odds of death after glioblastoma diagnosis in the United States by chemotherapeutic era

Bevacizumab (BZM) and temozolomide (TMZ) have been shown to be beneficial in the treatment of patients with glioblastoma. We sought evidence for the benefit of BZM in the general patient population at large. The Surveillance, Epidemiology, and End Results SEER database was queried for patients diagnosed with glioblastoma between 2000 and 2009, divided into a pre-TMZ era (January 2000-June 2003), a transitional era (July 2003-March 2005), a TMZ era (April 2005-October 2007), and a BZM-TMZ era (November 2007-December 2009). Binomial logit regression analyzed odds of death, taking into account age at diagnosis, tumor size, gender, race, marital status, radiotherapy, and extensive surgery. Compared with the pre-TMZ era, odds of death were decreased in the TMZ era by 12% (97.5% CI [confidence interval] 3-20%) 6 months after diagnosis and 36% (30-42%) a year after diagnosis; corresponding values for BZM-TMZ were 31% (24-37%) and 50% (45-55%). For era comparisons, decreases in odds of death were larger at 12 than 6 months; the opposite was true for extensive surgery and radiotherapy (P < 0.025, Wald χ(2) test, for each analysis). For both 6 and 12 month comparisons, odds of death in the BZM-TMZ era were lower than in the TMZ era (P < 0.025, Wald χ(2) test, for each analysis). The results provide evidence that TMZ positively impacted survival of glioblastoma patients and that the addition of BZM further improved survival, this lends support to the addition of BZM to the chemotherapeutic armamentarium. Evaluation of odds of death is an attractive alternative to Cox regression when proportional hazards assumptions are violated and follow-up is good.

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations

A total of 17 Y-specific STR loci were studied in 12 districts of the European part of Russia aiming to ascertain the amount of substructure required for the construction of a representative regional database. All groups exhibited high haplotype diversities but low inter-population variance as measured by an analysis of molecular variance. However, when Western Russia is taken as a whole, the genetic distances to the neighbouring populations were significant. Whereas gradual change in the Y chromosome pool exists between Russia and the Slavic-speaking populations to the West, remarkable discontinuities were observed with neighbouring populations in the East, North and South.