Medical students' self-perceived knowledge and clinical comfort with genetics in Pakistan.

Pakistan has a high rate of genetic disorders and neonatal mortality concurrent with noted lack of genetic counselors and geneticists. To meet the needs of the patient population, the responsibility of providing clinical genetic services falls on general and specialty physicians. However, their education regarding these essential services is not standardized in medical school curricula nor has it ever been evaluated. The purpose of this work is to describe the self-perceived knowledge, clinical comfort, and perspectives of Pakistani medical students toward their medical genetics' education. A web-based survey was distributed electronically to medical schools around the country. The survey comprised of four sections: (1) participant demographics, (2) self-perceived medical genetics knowledge, (3) level of comfort in applying genetic knowledge and skills, and (4) attitudes toward medical genetics education. Descriptive statistics and a one-way analysis of variance were used for data analysis. Medical students in years 3, 4, and 5 (n = 473) from 25 medical schools participated in this research representing medical education in four Pakistani provinces. Most medical students reported "minimal" to "basic" knowledge of genetic testing methodology (64.7%), cancer genetics (64.9%), prenatal genetic testing (63.02%), and treatment strategies for genetic disease (72.9%). A plurality of students (37%) reported they were uncomfortable with interpreting and communicating genetic test results to patients. Medical students also expressed dissatisfaction with their medical genetics (40%) and genetic counselors training (42%). The self-perceived knowledge and clinical comfort with genetics among Pakistani medical students was limited, especially regarding genetic testing. A significant portion (74.5%) expressed desire for additional genetics education during medical school to aid in their role as future physicians. It is important for physicians-in-training to have a solid understanding of genetic concepts, technologies, and genetic counseling to best support their patients. As endorsed by the participating medical students, this study supports inclusion of more robust genetics' education into Pakistan's medical school curricula.

Arginase deficiency masked by cerebral palsy and coagulopathy-Three varied presentations of Latin American origin.

Arginase deficiency (ARG1-D) is an autosomal recessive inborn error of metabolism that is often misdiagnosed. Classic presentation of ARG1-D includes progressive symptoms of spasticity, delayed development, cognitive impairment, protein avoidance, and seizures. Patients who present atypically may evade diagnosis and require a thoughtful diagnostic workup. Here, we discuss three females of Latin American origin with differing clinical presentations, but who all have the same intronic pathogenic variant in ARG1. Importantly, we found that each case included elevated coagulopathy on laboratory testing and discussed one case in particular with manifestation of bleeding. When diagnosed early, treatment is favorable and can prevent progressive decline. While many states have added ARG1-D to their expanded newborn screening panels, still many states and countries do not screen for ARG1-D, and it can be missed in a healthy newborn. We aim to bring awareness to not only the classic presentation as a necessary consideration for otherwise unexplained spastic diplegia but also to the varied presentations of ARG1-D.

Disability education and implications for genetic counselor training.

The genetic counseling (GC) community has faced criticism about the duality of promoting patient autonomy while also advocating for individuals with disabilities. This study assessed the attitudes of the disability community and GCs to identify content that should be included in GC disability education and evaluate the landscape of GC disability education. Members of the disability community and GCs completed an electronic survey distributed through electronic listservs and partnering organizations. A total of 672 responses were analyzed from both the disability community (n = 596) and the GC community (n = 76). Members of the disability community noted differences in GC comfort level discussing different aspects of disability with GCs being perceived as being very knowledgeable about medical aspects 71% of the time versus 49% of the time when discussing social/lifestyle aspects of disability. This discordance was reflected in GCs reported comfort level in discussing medical aspects (89%) and social aspects of disability (65%) during a session. Most GC respondents (71%) felt they received adequate knowledge during their disability education and variation was reported in the execution of disability education by training programs. Disability education content recommendations from the disability community and GCs included emphasizing four key aspects of disability: medical, social/lifestyle, lived experience, and the disability rights movement. Respondents of both cohorts stressed the inclusion of and exposure to persons with disabilities in disability education to understand the lived experience of persons with disabilities. The disability community identified additional disability education content to be included such as empathy training, family hardships, and mental health. The results of this study have practice implications and provide a foundation for training expectations to ensure future GCs possess the necessary skills to improve the quality of services provided to families and persons with disabilities.

Identifying the current status and future needs of clinical, educational, and laboratory genetics services in Pakistan: a web-based panel discussion.

While the prevalence of genetic disorders has been well documented in the Muslim-majority, low-socioeconomic country of Pakistan, the provision of medical genetic services remains limited and cost-prohibitive to the masses in the country. With the objective of identifying gaps in the provision of medical genetics services as perceived by the healthcare providers and the general public, the Pakistani Society of Medical Genetics and Genomics (PSMG) organized a needs assessment webinar on December 6, 2020, titled, "A Vibrant Discussion on the Current Status and Future Needs of Medical Genetic Services in Pakistan." The objectives of the webinar were (1) to explore the current availability of medical genetics services, (2) to identify areas in clinical genetics delivery models needed to improve the state of medical genetics in the country, and (3) to garner the interest in such provisions from the expert and lay audience. The webinar consisted of a moderator-led, structured interview of an expert panel including the following topics: (1) postgraduate clinical genetics and genetic counseling training programs, (2) medical genetics clinics and formal genetic counseling services), (3) clinical genetic testing and (4) patient support and advocacy groups. The webinar was followed by a short, web-based survey completed by 35 of the 60 attendees. The results of this survey indicated overwhelming support for establishing formal genetic counseling educational opportunities (91.6%) and increasing the availability of genetic testing (100%). This report further summarizes the opinions and recommendations of the panelists and the audience survey results.

Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort.

PURPOSE: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. METHODS: Clinical data was collected through an extensive web-based survey. RESULTS: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). CONCLUSION: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes.

Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability.

Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated (DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in DVL2. We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with FZD2 variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic NXN variants clustered together with the majority of probands carrying DVL1, DVL2, and DVL3 variants, demonstrating no phenotypic distinction between the NXN-autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing WNT5A, FZD2, and ROR2 apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.

Hypoglycemia in mitochondrial disorders.

Diabetes and hyperglycemia are common features of mitochondrial disorders. This study investigates the frequency of non-iatrogenic hypoglycemia in individuals with these disorders. Of 116 patients, 22 (18.97%) experienced at least two episodes of hypoglycemia. This rate is significantly higher (p < 0.05) than the 6% seen in the non-diabetic, general population. Neonatal readings were 30 mg/dL lower than non-neonatal readings. As hypoglycemia appears to occur frequently in individuals with mitochondrial disorders, with lower blood glucose levels in the neonatal period, early and continued monitoring of blood glucose is necessary. Also, mitochondrial disorders should be considered in cases of recurrent hypoglycemia.

Exploring the predicted yield of prenatal testing by evaluating a postnatal population with structural abnormalities using a novel mathematical model.

OBJECTIVE: To determine the yield of prenatal testing and screening options after identification of fetal structural abnormalities using a novel mathematical model. METHOD: A retrospective chart review was conducted to collect structural abnormality and genetic testing data on infants who were evaluated postnatally by a medical geneticist. A novel mathematical model was used to determine and compare the predicted diagnostic yields of prenatal testing and screening options. RESULTS: Over a quarter of patients with at least one structural abnormality (28.1%, n = 222) had a genetic aberration identified that explained their phenotype. Chromosomal microarray (CMA) had the highest predicted diagnostic yield (26.8%, P < .001). Karyotype (20.8%) had similar yields as genome wide NIPT (21.2%, P = .859) and NIPT with select copy number variants (CNVs) (17.9%, P = .184). Among individuals with an isolated structural abnormality, whole exome sequencing (25.9%) and CMA (14.9%) had the highest predicted yields. CONCLUSION: This study introduces a novel mathematical model for predicting the potential yield of prenatal testing and screening options. This study provides further evidence that CMA has the highest predicted diagnostic yield in cases with structural abnormalities. Screening with expanded NIPT options shows potential for patients who decline invasive testing, but only in the setting of adequate pre-test counseling.

The Impact of Psychiatric Symptoms on Tuberous Sclerosis Complex and Utilization of Mental Health Treatment.

BACKGROUND: Tuberous sclerosis complex (TSC) is a multisystem, neurocutaneous disorder with a spectrum of TSC-associated neuropsychiatric disorders. The most common neuropsychiatric manifestations in the pediatric and adult populations are cognitive concerns, depression, and anxiety. Previous research suggests that while 90% of individuals with TSC have some TSC-associated neuropsychiatric disorders features, only 20% receive treatment, leading to a 70% treatment gap. METHODS: This web-based study used validated measures in conjunction with researcher-designed questions to evaluate perception of disease severity, presence of anxiety and depression, and the utilization and barriers toward mental health services among adults with TSC. RESULTS: The Beck Anxiety Inventory, Beck Depression Inventory-II, and Brief Illness Perception Questionnaire indicated that our overall study population had mild symptoms of anxiety, minimal depression, and a moderate perception of disease severity. Notably, the difference between the median depression score for men and women was statistically significant with men scoring higher than women (P = 0.02). Of 69 respondents, 57% (n = 39) reported receiving mental health treatment at some point over their lifetime. In both the mental health treatment group and the nonmental health treatment group, cost was more often indicated as a barrier to accessing mental health resources (treatment group: cost = 51% and stigma = 21%; nontreatment group: cost = 27% and stigma = 20%). CONCLUSIONS: TSC disease severity had a moderate and low-moderate association with anxiety and depression, respectively. Regardless of past utilization, respondents had a positive outlook towards the use of mental health services with the major barrier being cost.

Managing Variant Interpretation Discrepancies in Hereditary Cancer: Clinical Practice, Concerns, and Desired Resources.

Variant interpretation is a complex process, and classification may vary between sources. This study aimed to determine the practice of cancer genetic counselors regarding discrepancies in variant interpretation and to identify concerns when counseling these discrepancies. An electronic survey was sent to genetic counselors in the NSGC Cancer Special Interest Group. The vast majority of counselors (93%) had seen a variant interpretation discrepancy in practice. A large majority (96%) of respondents indicated that they conducted their own research on reported variants. Most respondents cited variant databases as the most common resource utilized in researching variants. Approximately 33% of counselors spent 45 min or more of extra time researching a discrepancy compared to researching a variant with a single classification. When asked how they approached counseling sessions involving variant interpretation discrepancies, the free responses emphasized that counselors considered family history, clinical information, and psychosocial concerns, showing that genetic counselors tailored the session to each individual. Discrepancies in variant interpretation are an ongoing concern for clinical cancer genetic counselors, as demonstrated by the fact that counselors desired further resources to aid in addressing these discrepancies, including a centralized database (89%), guidelines from a major organization (88%), continuing education about the issue (74%), and functional studies (58%). Additionally, most respondents reported that the ideal database would be owned by a non-profit organization (59%) and obtain information directly from laboratories (91%). This investigation was the first to address these discrepancies from a clinical point of view. The study demonstrates that discrepancies in variant interpretation are a concern for clinical cancer genetic counselors and outlines the need for additional support.

Identification of novel candidate disease genes from de novo exonic copy number variants.

BACKGROUND: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS: In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS: Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.

Knowledge and Self-Esteem of Individuals with Neurofibromatosis Type 1 (NF1).

Neurofibromatosis Type 1 (NF1) is a progressive genetic disorder characterized by physical findings such as café-au-lait macules, Lisch nodules, and neurofibromas in addition to other medical complications. Learning and social problems are more prevalent among individuals affected with NF1. It has been reported that people with NF1 have lower self-esteem (SE) when compared to the general population. Additionally, a study published over 20 years ago found that overall knowledge of NF1 was lacking in individuals affected with the condition. The goals of our study were to evaluate NF1 knowledge in adolescents and adults with the condition, as well as to determine if there is a link between patient knowledge and SE. Furthermore, we explored the impact of other factors, such as attendance at a NF1 support group and having a family history of NF1, on knowledge and SE. A survey comprised of knowledge-based questions and the Rosenberg Self-Esteem Scale was distributed to individuals with NF1 through the Texas NF Foundation. Overall, the 49 respondents (13 to 73 years of age) had a mean knowledge score of 77.9 % correct answers. Consistent with previous studies, the SE of our study population was lower when compared to general population norms. Although no correlation between knowledge and SE was observed, SE scores were on average higher if a person reported the following: having friends with NF1 (p = 0.009); attending a NF1 support group (p = 0.006); receiving care at a NF clinic (p = 0.049); or having received genetic counseling (p = 0.008). Further research is needed to better understand the relationship between these factors and SE in the NF1 population.

The views of Pakistani doctors regarding genetic counseling services - is there a future?

Pakistan is a densely populated country in South Asia with a high burden of genetic disease. A dearth of medical genetic services exists and master's level trained genetic counselors (GCs) are currently not a part of the healthcare system. This study is the first to determine the views of Pakistani medical doctors (MDs) towards genetic counseling services in Pakistan, including what manner a master's level genetic counselor might be incorporated into the healthcare system. Fifty-one MDs practicing in the city of Karachi completed a self-administered survey of twenty questions. Of the 49 respondents who answered a specific question, 100 % (49/49) felt that they would refer at least some, if not all, of their relevant patients to a genetic's clinic if one existed in Karachi. Overall, the respondents showed a positive attitude towards the provision of genetic counseling services as a part of the healthcare system of Pakistan. Some of the proposed roles identified specifically for GCs included: explaining how Down syndrome occurs (66.1 %), discussing genes associated with breast cancer (77.4 %), and explaining the inheritance pattern of ß-thalassemia (65.5 %). In contrast, the review of medical and family history and discussion of medical procedures such as ultrasound and amniocentesis were typically seen as the role of a physician. A majority of the respondents (98 %) were in favor of premarital carrier screening for thalassemia and would refer patients to a GC to describe the importance of carrier screening (84.3 %) and to help explain carrier screening results (94.1 %). Many respondents selected GCs as the ideal provider of education and support for people with inherited conditions (43.8 %), followed by specialist MDs (26 %) and general physicians (22.9 %). Considering the high burden of genetic disease in the country, we encourage the development of genetic counseling services in Pakistan.