Clinically significant findings in a decade-long retrospective study of prenatal chromosomal microarray testing.

BACKGROUND: Chromosomal microarray (CMA) is commonly utilized in the obstetrics setting. CMA is recommended when one or more fetal structural abnormalities is identified. CMA is also commonly used to determine genetic etiologies for miscarriages, fetal demise, and confirming positive prenatal cell-free DNA screening results. METHODS: In this study, we retrospectively examined 523 prenatal and 319 products-of-conception (POC) CMA cases tested at Nationwide Children's Hospital from 2011 to 2020. We reviewed the referral indications, the diagnostic yield, and the reported copy number variants (CNV) findings. RESULTS: In our cohort, the diagnostic yield of clinically significant CNV findings for prenatal testing was 7.8% (n = 41/523) compared to POC testing (16.3%, n = 52/319). Abnormal ultrasound findings were the most common indication present in 81% of prenatal samples. Intrauterine fetal demise was the common indication identified in POC samples. The most common pathogenic finding observed in all samples was isolated trisomy 21, detected in seven samples. CONCLUSION: Our CMA study supports the clinical utility of prenatal CMA for clinical management and identifying genetic etiology in POC arrays. In addition, it provides insight to the spectrum of prenatal and POC CMA results as detected in an academic hospital clinical laboratory setting that serves as a reference laboratory.

A Decade's Experience in Pediatric Chromosomal Microarray Reveals Distinct Characteristics Across Ordering Specialties.

Chromosomal microarray (CMA) is a testing modality frequently used in pediatric patients; however, published data on its utilization are limited to the genetic setting. We performed a database search for all CMA testing performed from 2010 to 2020, and delineated the diagnostic yield based on patient characteristics, including sex, age, clinical specialty of providers, indication of testing, and pathogenic finding. The indications for testing were further categorized into Human Phenotype Ontology categories for analysis. This study included a cohort of 14,541 patients from 29 different medical specialties, of whom 30% were from the genetics clinic. The clinical indications for testing suggested that neonatology patients demonstrated the greatest involvement of multiorgan systems, involving the most Human Phenotype Ontology categories, compared with developmental behavioral pediatrics and neurology patients being the least. The top pathogenic findings for each specialty differed, likely due to the varying clinical features and indications for testing. Deletions involving the 22q11.21 locus were the top pathogenic findings for patients presenting to genetics, neonatology, cardiology, and surgery. Our data represent the largest pediatric cohort published to date. This study is the first to demonstrate the diagnostic utility of this assay for patients seen in the setting of different specialties, and it provides normative data of CMA results among a general pediatric population referred for testing because of variable clinical presentations.

Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience.

Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.

Alzheimer's disease development in adults with Down syndrome: Caregivers' perspectives.

Research about Alzheimer's disease (AD) in individuals with Down syndrome (DS) has predominantly focused on the underlying genetics and neuropathology. Few studies have addressed how AD risk impacts caregivers of adults with DS. This study aimed to explore the perceived impact of AD development in adults with DS on caregivers by assessing caregiver knowledge, concerns, effect on personal life, and resource utilization via a 40-question (maximum) online survey. Survey distribution by four DS organizations and two DS clinics resulted in 89 caregiver respondents. Only 28 caregivers correctly answered all three AD knowledge questions. Caregivers gave an average AD concern rating of 5.30 (moderately concerned) and an average impact of possible diagnosis rating of 6.28 (very strong impact), which had a significant negative correlation with the age of the adult with DS (p = .009). Only 33% of caregivers reported utilization of resources to gain more information about the AD and DS association, with low levels of perceived usefulness. Our data reveal caregivers' misconceptions about AD development in DS, underutilization of available resources, and substantial concerns and perceived impacts surrounding a possible AD diagnosis. This study lays the foundation for how the medical community can better serve caregivers of aging adults with DS.

An assessment of health, social, communication, and daily living skills of adults with Down syndrome.

Adults with Down syndrome (DS) are surviving longer, yet data delineating life skills are lacking. As providers are encouraged to provide a "balanced" description of DS to family members/caregivers, more quantitative data are required to accurately describe the abilities and potential of adults with DS. This study assessed health, social, communication, and daily living skills of adults with DS to describe the range of abilities and to show how increasing age contributes to functional abilities. Caregivers of an adult with DS 20 years of age or older participated in an online questionnaire. Descriptive statistics and scores from scales assessed relationships between the number of health issues reported and functional abilities, and how the abilities changed as age increased. Of 188 participants, 157 completed the survey with partial results included. Communication, independence, and social activity scores were compared to the number of congenital and non-congenital health issues reported. Linear regression results showed those with more health issues were significantly less likely to be independent and social. However, only current health issues affected communication skills. No significant correlation occurred between the number of congenital abnormalities and scores for independence/life skills as an adult. T-test by age group found decreasing abilities after 40 years of age. In conclusion, quantitative data and information from this study is beneficial for providers in order to describe the potential for an individual with DS and to assist caregivers to plan accordingly for the future of their adult with DS.

Pericentromeric regions of homozygosity on the X chromosome: Another likely benign population variant.

PURPOSE: While chromosomal regions of homozygosity (ROH) may implicate genes in known recessive disorders, their correlation to disease pathogenicity remains unclear. ROH around the centromere of the X chromosome (pericentromeric, pROH) is regarded as benign, although this has not been empirically demonstrated. METHODS: We examined microarray results from 122 female individuals harboring ROH bordering the X centromere. RESULTS: Consecutive ROH was most frequently observed for regions Xp11.23 to Xp11.21 and Xq11.1 to Xq12, with an average total size of 16.5 Mb. X chromosome pROH was unlikely related to phenotype in 41% (50/122) of cases due to other explanations: likely pathogenic deletion/duplication (17%, 21/122), apparently unaffected female (7%, 8/122), other clinical explanation (7%, 9/122), or consanguinity (10%, 12/122). Of the remaining cases with pROH as the only finding, four genes were associated with recessive disorders that overlapped one or more clinical features reported in our probands (KDM5C, FGD1, ZC4H2, and LAS1L). X chromosome pROH observed in our cohort overlapped with previously reported regions. CONCLUSIONS: pROH on the X chromosome are commonly observed in both affected individuals with alternate causes of disease as well as in unaffected individuals, suggesting that X chromosome pROH has no clinically significant effect on phenotype.