%0 Journal Article %J Genet Med %D 2020 %T CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. %A Bo Yuan %A Wang, Lei %A Liu, Pengfei %A Shaw, Chad %A Dai, Hongzheng %A Cooper, Lance %A Zhu, Wenmiao %A Anderson, Stephanie A %A Meng, Linyan %A Wang, Xia %A Wang, Yue %A Xia, Fan %A Xiao, Rui %A Braxton, Alicia %A Peacock, Sandra %A Schmitt, Eric %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Chiang, Theodore %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice %A Cheung, Sau Wai %A Bacino, Carlos A %A Eng, Christine M %A Yang, Yaping %A James R Lupski %A Bi, Weimin %K Child %K DNA Copy Number Variations %K Exome Sequencing %K Exons %K Humans %K INDEL Mutation %K Retrospective Studies %X

PURPOSE: Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort.

METHODS: We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders.

RESULTS: CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses.

CONCLUSIONS: AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.

%B Genet Med %V 22 %P 1633-1641 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32576985?dopt=Abstract %R 10.1038/s41436-020-0864-8 %0 Journal Article %J JAMA Pediatr %D 2017 %T Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. %A Meng, Linyan %A Pammi, Mohan %A Saronwala, Anirudh %A Magoulas, Pilar %A Ghazi, Andrew Ray %A Vetrini, Francesco %A Zhang, Jing %A He, Weimin %A Dharmadhikari, Avinash V %A Qu, Chunjing %A Ward, Patricia %A Braxton, Alicia %A Narayanan, Swetha %A Ge, Xiaoyan %A Tokita, Mari J %A Santiago-Sim, Teresa %A Dai, Hongzheng %A Chiang, Theodore %A Smith, Hadley %A Azamian, Mahshid S %A Robak, Laurie %A Bostwick, Bret L %A Schaaf, Christian P %A Potocki, Lorraine %A Scaglia, Fernando %A Bacino, Carlos A %A Hanchard, Neil A %A Wangler, Michael F %A Scott, Daryl %A Brown, Chester %A Hu, Jianhong %A Belmont, John W %A Burrage, Lindsay C %A Graham, Brett H %A Sutton, Vernon Reid %A Craigen, William J %A Plon, Sharon E %A Lupski, James R %A Beaudet, Arthur L %A Gibbs, Richard A %A Muzny, Donna M %A Miller, Marcus J %A Wang, Xia %A Leduc, Magalie S %A Xiao, Rui %A Liu, Pengfei %A Shaw, Chad %A Walkiewicz, Magdalena %A Bi, Weimin %A Xia, Fan %A Lee, Brendan %A Eng, Christine M %A Yang, Yaping %A Lalani, Seema R %K Adult %K Critical Care %K Disease Management %K Exome %K Exome Sequencing %K Genetic Counseling %K Genetic Diseases, Inborn %K Humans %K Infant %K Infant Care %K Infant, Newborn %K Intensive Care Units, Pediatric %K Length of Stay %K Retrospective Studies %K Texas %X

IMPORTANCE: While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined.

OBJECTIVE: To determine the diagnostic yield and use of clinical exome sequencing in critically ill infants.

DESIGN, SETTING, AND PARTICIPANTS: Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants.

MAIN OUTCOMES AND MEASURES: Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders.

RESULTS: The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling.

CONCLUSIONS AND RELEVANCE: Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.

%B JAMA Pediatr %V 171 %P e173438 %8 2017 Dec 04 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/28973083?dopt=Abstract %R 10.1001/jamapediatrics.2017.3438