Edward J. Lose

Clinically relevant single gene or intragenic deletions encompassing critical neurodevelopmental genes in patients with developmental delay, mental retardation, and/or autism spectrum disorders.

Recent studies suggest that copy number variations (CNVs) encompassing several genes involved in neurodevelopmental pathways are associated with a variety of neuropsychiatric phenotypes, including developmental delay (DD), mental retardation (MR), and autism spectrum disorders (ASDs). Here we present eight patients in a cohort of ∼1,200 patients referred for clinical array CGH testing for various neurodevelopmental phenotypes, who were identified to carry small (<1.0 Mb with the majority <500 kb) either total gene or intragenic deletions encompassing critical synaptic and other neurodevelopmental genes. The presentations of these patients included variable degrees of DD, speech problems, learning disabilities, MR, autistic‐like features, and mild non‐specific dysmorphic features. These genes belong to four functional categories, including neuronal transcription factor genes (NFIA at 1p31.3, MEF2C at 5q14.3, and CAMAT1 at 1p36.23p36.31), neuron‐specific splicing factor genes (RBFOX1 at 16p13.2p13.3), genes involved in synapse formation and maintenance (CNTNAP2 at 7q35 and LRFN5 at 14q21.2), and genes involved in neurotransmission (CHRNA7 at 15q13.3 and IL1RAPL1 at Xp21.2p21.3). Our report expands the list of neurodevelopmental genes deleted in various neurobehavioral phenotypes, expands the phenotypes caused by haploinsufficiency of previously reported critical neurodevelopmental genes, and elucidates the clinical relevance and need for careful clinical interpretation of some small CNVs <500 kb. This report also suggests that small clinically relevant deletions encompassing critical synaptic and other neurodevelopmental genes can present clinically with various neurobehavioral phenotypes, which implies the existence of overlapping neuronal pathways in the pathogenesis of these phenotypes.

Genomic diagnosis for children with intellectual disability and/or developmental delay

BackgroundDevelopmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-parent trios.MethodsWhole-exome sequences (WES) were generated for 365 individuals (127 affected) and whole-genome sequences (WGS) were generated for 612 individuals (244 affected).ResultsPathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11.3%). We found that a family history of neurological disease, especially the presence of an affected first-degree relative, reduces the pathogenic/likely pathogenic variant identification rate, reflecting both the disease relevance and ease of interpretation of de novo variants. We also found that improvements to genetic knowledge facilitated interpretation changes in many cases. Through systematic reanalyses, we have thus far reclassified 15 variants, with 11.3% of families who initially were found to harbor a VUS and 4.7% of families with a negative result eventually found to harbor a pathogenic or likely pathogenic variant. To further such progress, the data described here are being shared through ClinVar, GeneMatcher, and dbGaP.ConclusionsOur data strongly support the value of large-scale sequencing, especially WGS within proband-parent trios, as both an effective first-choice diagnostic tool and means to advance clinical and research progress related to pediatric neurological disease.

Recurrent ACADVL molecular findings in individuals with a positive newborn screen for very long chain acyl-coA dehydrogenase (VLCAD) deficiency in the United States

Very long chain acyl-coA dehydrogenase deficiency (VLCADD) is an autosomal recessive inborn error of fatty acid oxidation detected by newborn screening (NBS). Follow-up molecular analyses are often required to clarify VLCADD-suggestive NBS results, but to date the outcome of these studies are not well described for the general screen-positive population. In the following study, we report the molecular findings for 693 unrelated patients that sequentially received Sanger sequence analysis of ACADVL as a result of a positive NBS for VLCADD. Highlighting the variable molecular underpinnings of this disorder, we identified 94 different pathogenic ACADVL variants (40 novel), as well as 134 variants of unknown clinical significance (VUSs). Evidence for the pathogenicity of a subset of recurrent VUSs was provided using multiple in silico analyses. Surprisingly, the most frequent finding in our cohort was carrier status, 57% all individuals had a single pathogenic variant or VUS. This result was further supported by follow-up array and/or acylcarnitine analysis that failed to provide evidence of a second pathogenic allele. Notably, exon-targeted array analysis of 131 individuals screen positive for VLCADD failed to identify copy number changes in ACADVL thus suggesting this test has a low yield in the setting of NBS follow-up. While no genotype was common, the c.848T>C (p.V283A) pathogenic variant was clearly the most frequent; at least one copy was found in ~10% of all individuals with a positive NBS. Clinical and biochemical data for seven unrelated patients homozygous for the p.V283A allele suggests that it results in a mild phenotype that responds well to standard treatment, but hypoglycemia can occur. Collectively, our data illustrate the molecular heterogeneity of VLCADD and provide novel insight into the outcomes of NBS for this disorder.

Molecular cytogenetic characterization of two cases with constitutional distal 11q duplication/triplication†

Here, we report two cases with isolated distal 11q rearrangement and multiple congenital anomalies. The first patient is a two‐and‐a‐half year old male referred to our genetics clinic due to dysmorphic features and developmental delay including speech delay. Using conventional and molecular cytogenetic techniques, we demonstrate that he carries a recombinant chromosome with duplication of the 11q23.3q24.2 region resulting from an intrachromosomal insertion in the father. The second patient was originally reported by Partida‐Perez, et al. [Partida‐Perez et al., 2006 ] as having a tandem duplication of the 11q23.3 region. We performed array comparative genomic hybridization (aCGH) on this patient in order to map the exact region of the duplication, and demonstrated that the patient actually had a triplication within 11q23.3. We compare the clinical features of our two patients with those previously reported to further delineate the phenotype of isolated distal 11q duplication. Our study also demonstrates the clinical usefulness of whole genome high resolution aCGH analysis as a powerful molecular cytogenetic tool capable of detecting genomic imbalances due to cytogenetically visible but uncertain rearrangements.

Eliciting preferences on secondary findings: the Preferences Instrument for Genomic Secondary Results

Purpose:Eliciting and understanding patient and research participant preferences regarding return of secondary test results are key aspects of genomic medicine. A valid instrument should be easily understood without extensive pretest counseling while still faithfully eliciting patients’ preferences.Methods:We conducted focus groups with 110 adults to understand patient perspectives on secondary genomic findings and the role that preferences should play. We then developed and refined a draft instrument and used it to elicit preferences from parents participating in a genomic sequencing study in children with intellectual disabilities.Results:Patients preferred filtering of secondary genomic results to avoid information overload and to avoid learning what the future holds, among other reasons. Patients preferred to make autonomous choices about which categories of results to receive and to have their choices applied automatically before results are returned to them and their clinicians. The Preferences Instrument for Genomic Secondary Results (PIGSR) is designed to be completed by patients or research participants without assistance and to guide bioinformatic analysis of genomic raw data. Most participants wanted to receive all secondary results, but a significant minority indicated other preferences.Conclusions:Our novel instrument—PIGSR—should be useful in a wide variety of clinical and research settings.Genet Med 19 3, 337–344.

Clinical relevance of small copy-number variants in chromosomal microarray clinical testing

Purpose:The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (<500 kb) has not been well established in a clinical setting.Methods:We investigated the clinical significance of all nonpolymorphic small, nonrecurrent CNVs (<500 kb) in patients referred for CMA clinical testing over a period of 6 years, from 2009 to 2014 (a total of 4,417 patients). We excluded from our study patients with benign or likely benign CNVs and patients with only recurrent microdeletions/microduplications <500 kb.Results:In total, 383 patients (8.67%) were found to carry at least one small, nonrecurrent CNV, of whom 176 patients (3.98%) had one small CNV classified as a variant of uncertain significance (VUS), 45 (1.02%) had two or more small VUS CNVs, 20 (0.45%) had one small VUS CNV and a recurrent CNV, 113 (2.56%) had one small pathogenic or likely pathogenic CNV, 17 (0.38%) had two or more small pathogenic or likely pathogenic CNVs, and 12 (0.27%) had one small pathogenic or likely pathogenic CNV and a recurrent CNV. Within the pathogenic group, 80 of 142 patients (56% of all small pathogenic CNV cases) were found to have a single whole-gene or exonic deletion. The themes that emerged from our study are presented in the Discussion section.Conclusions:Our study demonstrates the diagnostic clinical relevance of small, nonrecurrent CNVs <500 kb during CMA clinical testing and underscores the need for careful clinical interpretation of these CNVs.Genet Med 19 4, 377–385.

The use by Alabama pediatricians of genetics consultation in the evaluation of developmental delay

Developmental delay (DD) is among the most common serious problems encountered by the general pediatrician. Published guidelines exist that recommend a genetics evaluation be a routine part of the evaluation of these children [Curry et al. (1997) Am J Med Genet 72:468–477; American Academy of Pediatrics (2001) Peds 108:192–195]. In an effort to determine if this recommendation is widely followed, we surveyed Alabama general pediatrics to learn how they utilize a genetic assessment in their evaluation of unexplained DD, and to identify any barriers to a genetics evaluation. A questionnaire was developed that asked about various factors that might influence how pediatricians use genetic evaluations. It was mailed to all members of the Alabama chapter of the American Academy of Pediatrics. The data were tabulated and analyzed by standard methods. One hundred thirty‐seven of 653 surveys were returned. The respondents were evenly divided among urban (35%), suburban (33%), and rural (32%) practice settings. Most were in a non‐academic group practice (71%) and not fellowship trained (76%). Most felt that a genetic evaluation will help define recurrence risk (96%), determine prognosis (96%), and guide patient management (95%). There was limited concern that a genetics evaluation would increase the cost of evaluation (24%) and that it would not eliminate unnecessary testing (64%). The most common indications for referral were the presence of birth defects (93%), positive family history of DD (88%), unusual facial appearance (88%), and parent request (71%). Poor growth was not as strong an indicator. Lack of meaningful results (20%) and expense (18%) were common reasons not to refer, and 48% also cited “other” reasons. Likelihood to refer did not differ by practice location (rural vs. suburban), but distance from a genetics center was a factor. Alabama general pediatricians appreciated the benefits of a genetic evaluation for DD, but several barriers were identified. These issues that must be addressed in order to make a genetics evaluation available to all children with DD.

The emerging role of primary care in genetics.

Purpose of review Advances in genetics are occurring at a rapid pace. It will ultimately be the primary care pediatrician who assimilates this knowledge and applies it to patient care. This article is written in a patient encounter format with which the pediatrician is familiar. The vignettes are from the authors own experiences in 13 years of general pediatric practice. Recent findings The current literature reinforces the idea that changes in the complexity of the diagnostic evaluation and the time spent explaining the recommended testing will be required by the pediatrician. With this responsibility comes the need of new training strategies for medical students and established pediatricians. Summary Pediatricians will be called upon to incorporate new genetic findings into patient care. This task will ultimately be no different than it was for past pediatricians to incorporate new immunizations or antibiotics into the care plan for each patient. Patient care will improve because therapy will be tailor-made for both the disease and the patient.

Genomic sequencing identifies secondary findings in a cohort of parent study participants

PurposeClinically relevant secondary variants were identified in parents enrolled with a child with developmental delay and intellectual disability.MethodsExome/genome sequencing and analysis of 789 “unaffected” parents was performed.ResultsPathogenic/likely pathogenic variants were identified in 21 genes within 25 individuals (3.2%), with 11 (1.4%) participants harboring variation in a gene defined as clinically actionable by the American College of Medical Genetics and Genomics. These 25 individuals self-reported either relevant clinical diagnoses (5); relevant family history or symptoms (13); or no relevant family history, symptoms, or clinical diagnoses (7). A limited carrier screen was performed yielding 15 variants in 48 (6.1%) parents. Parents were also analyzed as mate pairs (n = 365) to identify cases in which both parents were carriers for the same recessive disease, yielding three such cases (0.8%), two of which had children with the relevant recessive disease. Four participants had two findings (one carrier and one noncarrier variant). In total, 71 of the 789 enrolled parents (9.0%) received secondary findings.ConclusionWe provide an overview of the rates and types of clinically relevant secondary findings, which may be useful in the design and implementation of research and clinical sequencing efforts to identify such findings.

AsktheGeneticist SM : five years of online experience

Purpose: To identify the genetic informational needs and assess the level of awareness about clinical genetic services among adults who use the internet.Methods: We created an online service called AsktheGeneticistSM (http://www.askthegen.org) to answer questions about medical genetics. Since 2003, we have received 4497 questions from every US state and 84 countries/territories. Genetic counselors draft answers to the questions submitted. The questions and answers are next reviewed by clinical geneticists, then organized by topic and uploaded to the site. A link to an online website-user satisfaction survey is e-mailed to the user with a link to their Q&A.Results: Before visiting AsktheGeneticistSM, 20% (50/247) of survey respondents were unaware that genetic services existed. After visiting our website, 23.5% (58) of survey respondents sought contact with a genetics health care professional, compared with <1% of patients who self-refer to a general genetics clinic (binomial test; P < 0.0001). Website users most often sought information about a known genetic condition in their family and the risk of recurrence.Conclusions: Our data suggest that the internet can be an effective tool for increasing the awareness of genetic services and identifying genetic informational needs of online adults, as well as for connecting patients with genetic services.