Shweta U. Dhar

Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements

Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organisms life cycle.

22q13.3 Deletion Syndrome: Clinical and Molecular Analysis Using Array CGH

The 22q13.3 deletion syndrome results from loss of terminal segments of varying sizes at 22qter. Few genotype–phenotype correlations have been found but all patients have mental retardation and severe delay, or absence of, expressive speech. We carried out clinical and molecular characterization of 13 patients. Developmental delay and speech abnormalities were common to all and comparable in frequency and severity to previously reported cases. Array‐based comparative genomic hybridization showed the deletions to vary from 95 kb to 8.5 Mb. We also carried out high‐resolution 244K array comparative genomic hybridization in 10 of 13 patients, that defined the proximal and distal breakpoints of each deletion and helped determine the size, extent, and gene content within the deletion. Two patients had a smaller 95 kb terminal deletion with breakpoints within the SHANK3 gene while three other patients had a similar 5.5 Mb deletion implying the recurrent nature of these deletions. The two largest deletions were found in patients with ring chromosome 22. No correlation could be made with deletion size and phenotype although complete/partial SHANK3 was deleted in all patients. There are very few reports on array comparative genomic hybridization analysis on patients with the 22q13.3 deletion syndrome, and we aim to accurately characterize these patients both clinically and at the molecular level, to pave the way for further genotype–phenotype correlations.

Genetic Testing and Cancer Risk Management Recommendations by Physicians for At-Risk Relatives

Purpose: Sequence-based cancer susceptibility testing results are described as negative, deleterious mutation or variant of uncertain significance. We studied the impact of different types of test results on clinical decision making.Methods: Practicing physicians from five specialties in Texas completed an online case-based survey (n = 225). Respondents were asked to make genetic testing and management recommendations for healthy at-risk relatives of patients with cancer.Results: When the patient carried a deleterious BRCA1 mutation or variant of uncertain significance, 98% and 82% of physicians, respectively, recommended testing of at-risk relatives (P < 0.0001). In both situations, comprehensive BRCA1/2 analysis was selected most with a corresponding 9-fold increase in unnecessary genetic testing costs. There was no difference in physicians with (n = 81) or without (n = 144) prior BRCA1/2 testing experience (P = 0.3869). Cancer risk management recommendations were most intense for the relative with a deleterious mutation compared with variant of uncertain significance, negative, or no testing with 63%, 13%, 5%, and 2%, respectively, recommending oophorectomy (P < 0.0001).Conclusions: Independent of experience, or specialty, physicians chose more comprehensive testing for healthy relatives than current guidelines recommend. In contrast, management decisions demonstrated the uncertainty associated with a variant of uncertain significance. Utilization of genetic professionals and education of physicians on family-centered genetic testing may improve efficacy and substantially reduce costs.

Molecular diagnostic experience of whole-exome sequencing in adult patients

Purpose:Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults.Methods:We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms.Results:Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18–30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses.Conclusion:Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678–685.

Expanded clinical and molecular spectrum of guanidinoacetate methyltransferase (GAMT) deficiency.

Guanidinoacetate methyltransferase (GAMT) deficiency is a disorder of creatine biosynthesis, characterized by excessive amounts of guanidinoacetate in body fluids, deficiency of creatine in the brain, and presence of mutations in the GAMT gene. We present here 8 new patients with GAMT deficiency along with their clinical, biochemical and molecular data. The age at diagnosis of our patients ranges from 0 to 14 years. The age of onset of seizures usually ranges from infancy to 3 years. However, one of our patients developed seizures at age 5; progressing to myoclonic epilepsy at age 8 years and another patient has not developed seizures at age 17 years. Five novel mutations were identified: c.37ins26 (p.G13PfsX38), c.403G>T (p.D135Y), c.507_521dup15 (p.C169_S173dup), c.402C>G (p.Y134X) and c.610_611delAGinsGAA (p.R204EfsX63). Six patients had the c.327G>A (last nucleotide of exon 2) splice-site mutation which suggests that this is one of the most common mutations in the GAMT gene, second only to the known Portuguese founder mutation, c.59G>C (p.W20S). Our data suggests that the clinical presentation can be variable and the diagnosis may be overlooked due to unawareness of this disorder. Therefore, GAMT deficiency should be considered in the differential diagnosis of progressive myoclonic epilepsy as well as in unexplained developmental delay or regression with dystonia, even if the patient has no history of seizures. As more patients are reported, the prevalence of GAMT deficiency will become known and guidelines for prenatal diagnosis, newborn screening, presymptomatic testing and treatment, will need to be formulated.

Enhancing exposure to genetics and genomics through an innovative medical school curriculum

Purpose: Physicians entering medical practice in the 21st century will require more than a basic understanding of human genetics because of rapid progress in the field of genetics and genomics. The current undergraduate medical curriculum at most institutions is not adequate to prepare medical students for these challenges. Enhancing exposure to genetics throughout the medical school curriculum should help prepare the next generation of physicians to use genetic and genomic information for optimal patient care.Methods: We have introduced a Genetics Track Curriculum to the undergraduate medical curriculum at Baylor College of Medicine.Results: This track runs in parallel to the existing 4-year curriculum and includes didactic sessions, small group discussions, longitudinal clinical experiences, clinical and laboratory rotations, community outreach, and scholarly projects related to genetics. It also provides the students a means to network and discuss topics and career paths in medical genetics.Conclusion: We have developed a novel curriculum that enhances genomic education for medical students with the ultimate goal of enabling our graduates to deliver more effective and personalized medical care. We believe that the Genetics Track Curriculum at Baylor College of Medicine can serve as a prototype for other medical schools across the country and abroad.Genet Med 2012:14(1):163–167.

Autism genetic testing: a qualitative study of awareness, attitudes, and experiences among parents of children with autism spectrum disorders

Purpose:The goal of this first-of-its-kind qualitative study was to examine the awareness, attitudes, and experiences among parents of autistic children regarding autism genetic testing.Methods:We conducted in-depth, individual, and semistructured interviews with 42 parents of autistic children with diverse racial/ethnic backgrounds. All interviews were audio-taped, transcribed, and coded into major themes and subthemes.Results:Approximately one-quarter of participants had two or more autistic children, and about half of them were ethnic/racial minorities. The majority of participants postulated favorable attitudes toward autism genetic testing for three main reasons: early intervention and treatment, identifying the etiology of autism, and informed family planning. Nevertheless, among parents who had taken their children for genetic testing, some expressed frustration and questioned the competency of their providers in interpreting test results. Asian parents and those with a low socioeconomic status expressed lower awareness and tended to have more limited access to autism genetic testing.Conclusion:As health-care providers play a vital role in providing genetic services and education, these professionals should be educated and be sensitive to the needs of parents with autistic children. Further quantitative research is required to examine the effects of socio-demographic factors on parents’ awareness, attitudes, and experiences regarding autism genetic testing.Genet Med 2013:15(4):274–281

WDR35 mutation in siblings with Sensenbrenner syndrome: a ciliopathy with variable phenotype.

Sensenbrenner syndrome and unclassified short rib‐polydactyly conditions are ciliopathies with overlapping phenotypes and genetic heterogeneity. Mutations in WDR35 were identified recently in a sub‐group of patients with Sensenbrenner syndrome and in a single family that presented with an unclassified form of short‐rib polydactyly (SRP) syndrome. We report on siblings with an unusual combination of phenotypes: narrow thorax, short stature, minor anomalies, developmental delay, and severe hepatic fibrosis leading to liver failure and early death in two of the children. Both parents were unaffected suggesting autosomal recessive inheritance. The family and their affected children were followed over a decade. Exome sequencing was performed in one affected individual. It showed a homozygous missense mutation in a highly conserved position of the WDR35 gene. This family represents a WDR35‐ciliopathy with a complex clinical presentation that includes significant overlap of the phenotypes described in Sensenbrenner syndrome and the unclassified SRPs. The accurate molecular diagnosis of this family exemplifies the power of exome sequencing in the diagnosis of Mendelian disorders and enabled us to broaden and refine our understanding of Sensenbrenner syndrome and SRP. Detailed genotype–phenotype information is provided as well as discussion of previously reported cases.

A recurrent p.Arg92Trp variant in steroidogenic factor-1 (NR5A1) can act as a molecular switch in human sex development

Cell lineages of the early human gonad commit to one of the two mutually antagonistic organogenetic fates, the testis or the ovary. Some individuals with a 46,XX karyotype develop testes or ovotestes (testicular or ovotesticular disorder of sex development; TDSD/OTDSD), due to the presence of the testis-determining gene, SRY. Other rare complex syndromic forms of TDSD/OTDSD are associated with mutations in pro-ovarian genes that repress testis development (e.g. WNT4); however, the genetic cause of the more common non-syndromic forms is unknown. Steroidogenic factor-1 (known as NR5A1) is a key regulator of reproductive development and function. Loss-of-function changes in NR5A1 in 46,XY individuals are associated with a spectrum of phenotypes in humans ranging from a lack of testis formation to male infertility. Mutations in NR5A1 in 46,XX women are associated with primary ovarian insufficiency, which includes a lack of ovary formation, primary and secondary amenorrhoea as well as early menopause. Here, we show that a specific recurrent heterozygous missense mutation (p.Arg92Trp) in the accessory DNA-binding region of NR5A1 is associated with variable degree of testis development in 46,XX children and adults from four unrelated families. Remarkably, in one family a sibling raised as a girl and carrying this NR5A1 mutation was found to have a 46,XY karyotype with partial testicular dysgenesis. These unique findings highlight how a specific variant in a developmental transcription factor can switch organ fate from the ovary to testis in mammals and represents the first missense mutation causing isolated, non-syndromic 46,XX testicular/ovotesticular DSD in humans.

Tetrasomy 13q mosaicism associated with phylloid hypomelanosis and precocious puberty

Various forms of pigmentary dysplasias have been known to be associated with chromosomal mosaicism. One of these disorders, known as phylloid hypomelanosis, has been found to be predominantly associated with abnormalities in chromosome 13. Most of the reported literature involves mosaic trisomy 13 with clinical evidence of abnormal pigmentation in the form of leaf‐like or oblong achromic macules following Blaschkos lines. Here, we report on an 8‐year‐old girl with phylloid hypomelanosis and precocious puberty who was found to have mosaicism for tetrasomy 13q in the form of inverted dup(13)(q21) on her skin fibroblasts as well as peripheral blood karyotype. A higher resolution (244K) chromosomal microarray was done on DNA from skin fibroblasts confirming the breakpoint and gain of distal 13q, which made her tetrasomic for 13q21‐qter. This is the first‐ever reported association of tetrasomy 13q with phylloid hypomelanosis and precocious puberty. Our report further emphasizes the need to exclude any type of abnormalities of chromosome 13 in patients with phylloid hypopigmentation.