Genetic aspects of birth defects: new understandings of old problems

Biogeographic Ancestry Analysis of Microtia Patients in Colombia using Nonlinear Probabilistic Clustering

Population composition is crucial in exploring genetic associations and investigating conditions and diseases. Single nucleotide polymorphisms (SNPs) are the subject of extensive studies, as they represent the most prevalent genetic variability in the human population. This work proposes a hierarchical framework for nonlinear probabilistic clustering of individuals with mixed ancestry population components. Through methods such as Kernel PCA, latent variables that can capture complex patterns of genetic variation are found. Gaussian mixture clustering allows for the inference of the population structure of the data obtained through the proposed feature extraction model. The proposed method is trained with pure populations from Africa, Europe, East Asia, and America, achieving an adjusted rand index of 0.981 for the evaluation set. Validation is achieved by evaluating the method on real data sets and compared with results from previous studies, achieving a Mean Squared Error of 2.77%. The model was tested on Colombian individuals diagnosed with microtia, revealing a robust association between the prevalence of the Native American population component and their conditions.

Germline genome editing of human IVF embryos should not be subject to overly stringent restrictions

This paper critiques the restrictive criteria for germline genome editing recently proposed by Chin, Nguma, and Ahmad in this journal. While praising the authors for resisting fervent calls for an outright ban on clinical applications of the technology, this paper argues that their approach is nevertheless unduly restrictive, and may thus hinder technological progress. This response advocates for weighing potential benefits against risks without succumbing to excessive caution, proposing that ethical oversight combined with genetic scrutiny at the embryo stage post-editing can enable responsible use of the technology, ultimately reducing the burden of genetic diseases and enhancing human health, akin to how IVF transformed reproductive medicine despite strong initial opposition.

Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism

Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.

Effect of Whole-Genome Sequencing on the Clinical Management of Acutely Ill Infants With Suspected Genetic Disease: A Randomized Clinical Trial

IMPORTANCE

Whole-genome sequencing (WGS) shows promise as a first-line genetic test for acutely ill infants, but widespread adoption and implementation requires evidence of an effect on clinical management.

OBJECTIVE

To determine the effect of WGS on clinical management in a racially and ethnically diverse and geographically distributed population of acutely ill infants in the US.

DESIGN, SETTING, AND PARTICIPANTS

This randomized, time-delayed clinical trial enrolled participants from September 11, 2017, to April 30, 2019, with an observation period extending to July 2, 2019. The study was conducted at 5 US academic medical centers and affiliated children's hospitals. Participants included infants aged between 0 and 120 days who were admitted to an intensive care unit with a suspected genetic disease. Data were analyzed from January 14 to August 20, 2020.

INTERVENTIONS

Patients were randomized to receive clinical WGS results 15 days (early) or 60 days (delayed) after enrollment, with the observation period extending to 90 days. Usual care was continued throughout the study.

MAIN OUTCOMES AND MEASURES

The main outcome was the difference in the proportion of infants in the early and delayed groups who received a change of management (COM) 60 days after enrollment. Additional outcome measures included WGS diagnostic efficacy, within-group COM at 90 days, length of hospital stay, and mortality.

RESULTS

A total of 354 infants were randomized to the early (n = 176) or delayed (n = 178) arms. The mean participant age was 15 days (IQR, 7-32 days); 201 participants (56.8%) were boys; 19 (5.4%) were Asian; 47 (13.3%) were Black; 250 (70.6%) were White; and 38 (10.7%) were of other race. At 60 days, twice as many infants in the early group vs the delayed group received a COM (34 of 161 [21.1%; 95% CI, 15.1%-28.2%] vs 17 of 165 [10.3%; 95% CI, 6.1%-16.0%]; P = .009; odds ratio, 2.3; 95% CI, 1.22-4.32) and a molecular diagnosis (55 of 176 [31.0%; 95% CI, 24.5%-38.7%] vs 27 of 178 [15.0%; 95% CI, 10.2%-21.3%]; P < .001). At 90 days, the delayed group showed a doubling of COM (to 45 of 161 [28.0%; 95% CI, 21.2%-35.6%]) and diagnostic efficacy (to 56 of 178 [31.0%; 95% CI, 24.7%-38.8%]). The most frequent COMs across the observation window were subspecialty referrals (39 of 354; 11%), surgery or other invasive procedures (17 of 354; 4%), condition-specific medications (9 of 354; 2%), or other supportive alterations in medication (12 of 354; 3%). No differences in length of stay or survival were observed.

CONCLUSIONS AND RELEVANCE

In this randomized clinical trial, for acutely ill infants in an intensive care unit, introduction of WGS was associated with a significant increase in focused clinical management compared with usual care. Access to first-line WGS may reduce health care disparities by enabling diagnostic equity. These data support WGS adoption and implementation in this population.

TRAIL REGISTRATION

ClinicalTrials.gov Identifier: NCT03290469.

Evaluation and Risk Assessment of Congenital Anomalies in Neonates

Congenital anomalies (CA) are a large heterogeneous group of disorders of abnormal morphogenesis or biochemistry which present at birth and carry widely variable implications for morbidity and mortality. They are the leading cause of infant mortality in the USA, with an incidence of 3-4% of all births. CA are the fourth leading cause of neonatal mortality worldwide, with an estimated 295,000 deaths annually. The enormous variability in the clinical presentation in terms of severity, time of occurrence, course, complications, management, and outcomes makes the evaluation of CA complicated, highly specific, and individualized. The anomalies can impart tremendous physical, social, and emotional distress on the patient with massive emotional, social, financial, and medical implications for the family and society. The diagnosis may remain elusive despite rigorous, elaborate, and extensive investigations in many cases. While the enormous strides in genetic testing and gene modification therapy have an encouraging impact on the diagnosis and treatment, the risk assessment of recurrence in the family and population of CA remains obscure in most cases due to the lack of information and referable evidence.

Cancer Risk by Attained Age among Children with Birth Defects in Arkansas

BACKGROUND

Few studies have evaluated associations between birth defects and risk of pediatric cancers by age of attainment. Therefore, we assessed the risk of cancer among children with and without birth defects by age at attainment.

METHODS

We examined cancer risk in children ≤14 years with and without birth defects born between 1996 and 2011 by linking data from the Arkansas Reproductive Health Monitoring System, Arkansas Central Cancer Registry, and birth certificates. Age of attainment for cancer was calculated as person-years from birth to cancer diagnosis, death, or end of study period, whichever occurred first. Using Cox proportional hazards models, we evaluated associations by attained age groups (<1, 1-4, 5-9, and 10-14 years) between: (1) groups of birth defects (any, chromosomal, and non-chromosomal) and any cancer; (2) non-chromosomal birth defects by organ system and any cancer; and (3) non-chromosomal birth defects and subtypes of cancer.

RESULTS

In the cohort of 629,086 children, 23,341 (3.7%) children had birth defects and 1,037 (0.2%) children had cancer. For children with non-chromosomal birth defects, specifically cardiovascular and genitourinary, highest risk of any cancer was observed in first year of life (Hazard Ratio [HR] 18.5; 95% confidence interval [CI] 10.1-33.8). For children with chromosomal birth defects, increased cancer risk was observed among those 1-4 years-old (HR 20.0; 95% CI 8.3-48.4).

CONCLUSION

Overall, cancer risk among children with birth defects was highest among those <5 years-old. Our findings, consistent with previous studies, may inform surveillance strategies for children with birth defects.

High Mutation Levels are Compatible with Normal Embryonic Development in Mlh1-Deficient Mice

To elucidate the role of the mismatch repair gene Mlh1 in genome instability during the fetal stage, spontaneous mutations were studied in Mlh1-deficient lacZ-transgenic mouse fetuses. Mutation levels were high at 9.5 days post coitum (dpc) and gradually increased during the embryonic stage, after which they remained unchanged. In addition, mutations that were found in brain, liver, spleen, small intestine and thymus showed similar levels and no statistically significant difference was found. The molecular nature of mutations at 12.5 dpc in fetuses of Mlh1+/+ and Mlh1-/- mice showed their own unique spectra, suggesting that deletion mutations were the main causes in the deficiency of the Mlh1 gene. Of note, fetuses of irradiated mice exhibited marked differences such as post-implantation loss and Mendelian distribution. Collectively, these results strongly suggest that high mutation ofMlh1-/--deficient fetuses has little effect on the fetuses during their early developmental stages, whereas Mlh1-/--deficient fetuses from X-ray irradiated mothers are clearly effected.

Role of the Msh2 gene in genome maintenance and development in mouse fetuses

In an attempt to evaluate the roles of the mismatch repair gene Msh2 in genome maintenance and in development during the fetal stage, spontaneous mutations and several developmental indices were studied in Msh2-deficient lacZ-transgenic mouse fetuses. Mutation levels in fetuses were elevated at 9.5 dpc (days post coitum) when compared to wild-type mice, and the level of mutations continued to increase until the fetuses reached the newborn stage. The mutation levels in 4 different tissues of newborns showed similar magnitudes to those in the whole body. The levels remained similar after birth until 6 months of age. The molecular nature of the mutations examined in 12.5 dpc fetuses of Msh2(+/+) and Msh2(-/-) revealed unique spectra which reflect errors produced during the DNA replication process, and those corrected by a mismatch repair system. Most base substitutions and simple deletions were reduced by the presence of the Msh2 gene, whereas G:C to A:T changes at CpG sequences were not affected, suggesting that the latter change was not influenced by mismatch repair. On the other hand, analysis of developmental indices revealed that there was very little effect, including the presence of malformations, resulting from Msh2-deficiencies. These results indicate that elevated mutation levels have little effect on the development of the fetus, even if a mutator phenotype appears at the organogenesis stage.

Genetic and Non Genetic Aspects of Autism Spectrum Disorders

Chromosome abnormalities have long been recognized as an important cause of learning disabilities and multiple malformation syndromes. About 0.8% of live born infants have numerical or structural chromosomal anomalies that result in an abnormal phenotype. Identification of such anomalies is important clinically and also for accurate genetic counseling. Recently, molecular cytogenetic and array-based techniques have enabled higher resolution screens for chromosome anomalies. This brief review of the etiology of autism spectrum disorders (ASD) focuses on the heritable and non heritable risk factors that underlie this major neuro-developmental disorder. Since all patients with a chromosomal imbalance are dysmorphic, the association of ASD with a facial dysmorphism seems to be a good indication for chromosomal anomaly screening.