%0 Journal Article %J Hum Mutat %D 2022 %T A recurrent single-exon deletion in TBCK might be under-recognized in patients with infantile hypotonia and psychomotor delay. %A Dai, Hongzheng %A Zhu, Wenmiao %A Bo Yuan %A Walley, Nicole %A Schoch, Kelly %A Jiang, Yong-Hui %A Phillips, John A %A Jones, Melissa S %A Liu, Pengfei %A David R Murdock %A Burrage, Lindsay C %A Lee, Brendan %A Rosenfeld, Jill A %A Xiao, Rui %K DNA Copy Number Variations %K Exome %K Exome Sequencing %K Exons %K Humans %K Infant %K Muscle Hypotonia %K Muscular Diseases %K Protein Serine-Threonine Kinases %K Retrospective Studies %X

Advanced bioinformatics algorithms allow detection of multiple-exon copy-number variations (CNVs) from exome sequencing (ES) data, while detection of single-exon CNVs remains challenging. A retrospective review of Baylor Genetics' clinical ES patient cohort identified four individuals with homozygous single-exon deletions of TBCK (exon 23, NM_001163435.2), a gene associated with an autosomal recessive neurodevelopmental phenotype. To evaluate the prevalence of this deletion and its contribution to disease, we retrospectively analyzed single nucleotide polymorphism (SNP) array data for 8194 individuals undergoing ES, followed by PCR confirmation and RT-PCR on individuals carrying homozygous or heterozygous exon 23 TBCK deletions. A fifth individual was diagnosed with the TBCK-related disorder due to a heterozygous exon 23 deletion in trans with a c.1860+1G>A (NM_001163435.2) pathogenic variant, and three additional heterozygous carriers were identified. Affected individuals and carriers were from diverse ethnicities including European Caucasian, South Asian, Middle Eastern, Hispanic American and African American, with only one family reporting consanguinity. RT-PCR revealed two out-of-frame transcripts related to the exon 23 deletion. Our results highlight the importance of identifying single-exon deletions in clinical ES, especially for genes carrying recurrent deletions. For patients with early-onset hypotonia and psychomotor delay, this single-exon TBCK deletion might be under-recognized due to technical limitations of ES.

%B Hum Mutat %V 43 %P 1816-1823 %8 2022 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/36317458?dopt=Abstract %R 10.1002/humu.24497 %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 (nā€‰=ā€‰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