The Role of Preprocedure Genetic Counseling in Pregnancies Interrupted for Fetal Abnormalities.

OBJECTIVE: Congenital birth defects affect 3 to 5% of pregnancies. Genetic counseling can help patients navigate the testing process and understand results. The study objective was to identify predictors and utility of genetic counseling at the time of pregnancy termination. Additionally, we aimed to see what proportion of patients would benefit from additional testing based on the results of the genetic testing. STUDY DESIGN: This was a retrospective cohort review of all terminations performed for fetal anomalies by an academic center from July 2016 to May 2020. Indications were stratified by abnormal serum screening or types of abnormal ultrasound findings. Data were abstracted regarding uptake of genetic counseling and testing results. Abnormal results that warranted additional testing regarding recurrence risks were noted. Multivariable logistic regression was performed to identify predictors of receipt of genetic counseling and testing. RESULTS: Of 387 patients, 57% (n = 220) received preprocedure genetic counseling and 43% (n = 167) did not. Among patients who received diagnostic testing, 62% (n = 194) had genetic counseling compared with 38% (n = 121) without counseling (adjusted odds ratio 2.46, 95% confidence interval [1.41-4.29], p < 0.001). Among the entire cohort, 38% (n = 148) had suspected aneuploidy based on serum screening. Of these, 89% (n = 132/148) had definitive testing, 92% (n = 122/132) confirming the aneuploidy. Among the other 68% (n = 239) with structural anomalies, 76% (n = 183) had diagnostic testing with 29% (n = 53) yielding an abnormal result. Among those fetuses with structural anomalies, 36% (n = 19/53) of genetic diagnoses warranted additional parental testing because of risk of recurrence compared with only 2% (n = 2/122) of patients with abnormal serum screening results alone. CONCLUSION: Genetic counseling was associated with increased uptake of diagnostic testing, which yielded useful information and prompted additional testing. This is important for determining etiology and recurrence risk and should be offered to patients presenting for termination for fetal indications, as well as providing diagnostic closure for patients. KEY POINTS: · Genetic counseling increases the uptake of diagnostic testing in patients with fetal anomalies.. · Patients with ultrasound anomalies received less diagnostic testing despite actionable results 36% of the time.. · Genetic testing is invaluable for recurrence risk counseling even if patients chose to terminate..

Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report.

While molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans. Differences in NGS panel size, use, and gene content were reported. Gene content for myeloid processes was reported to be generally excellent, while genes for lymphoid processes were less well covered. The turnaround time (TAT) for acute cases, including acute myeloid leukemia, was reported to range from 2 to 7 calendar days to 15 to 21 calendar days, with different approaches to achieving rapid TAT described. To help guide NGS panel design and standardize gene content, consensus gene lists based on current and future NGS panels in development were generated. Most survey respondents expected molecular testing at academic laboratories to continue to be viable in the future, with rapid TAT for acute cases likely to remain an important factor. Molecular testing reimbursement was reported to be a major concern. The results of this survey and subsequent discussions improve the shared understanding of differences in testing practices for hematologic malignancies between institutions and will help provide a more consistent level of patient care.

Outcomes of two different unbalanced segregations from a maternal t(4;10)(q33;p15.1) translocation.

BACKGROUND: Unbalanced translocations can cause developmental delay (DD), intellectual disability (ID), growth problems, dysmorphic features, and congenital anomalies. They may arise de novo or may be inherited from a parent carrying a balanced rearrangement. It is estimated that 1/500 people is a balanced translocation carrier. The outcomes of different chromosomal rearrangements have the potential to reveal the functional consequences of partial trisomy or partial monosomy and can help guide genetic counseling for balanced carriers, and other young patients diagnosed with similar imbalances. METHODS: We performed clinical phenotyping and cytogenetic analyses of two siblings with a history of developmental delay (DD), intellectual disability (ID) and dysmorphic features. RESULTS: The proband, a 38-year-old female, has a history of short stature, dysmorphic features and aortic coarctation. She underwent chromosomal microarray analysis, which identified partial monosomy of 4q and partial trisomy of 10p. Her brother, a 37-year-old male, has a history of more severe DD, behavioral problems, dysmorphic features, and congenital anomalies. Subsequently, karyotype confirmed two different unbalanced translocations in the siblings: 46,XX,der(4)t(4;10)(q33;p15.1) and 46,XY,der(10)t(4;10)(q33;p15.1), respectively. These chromosomal rearrangements represent two possible outcomes from a parent who is a carrier for a balanced translocation 46,XX,t(4;10)(q33;p15.1). CONCLUSION: To our knowledge, this 4q and 10p translocation has not been described in literature. In this report we compare clinical features due to the composite effects of partial monosomy 4q with partial trisomy 10p and partial trisomy 4q with partial monosomy 10p. These findings speak to the relevance of old and new genomic testing, the viability of these segregation outcomes, and need for genetic counseling.

Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU.

With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.

Evidence-based review of genomic aberrations in diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS): Report from the cancer genomics consortium lymphoma working group.

Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). The 2016 World Health Organization (WHO) classification defined DLBCL, NOS and its subtypes based on clinical findings, morphology, immunophenotype, and genetics. However, even within the WHO subtypes, it is clear that additional clinical and genetic heterogeneity exists. Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. We gathered an international group of experts to review the current literature on DLBCL, NOS, with respect to genomic aberrations and the role they may play in the diagnosis, prognosis and therapeutic decisions. We comprehensively surveyed clinical laboratory directors/professionals about their genetic testing practices for DLBCL, NOS. The survey results indicated that a variety of diagnostic approaches were being utilized and that there was an overwhelming interest in further standardization of routine genetic testing along with the incorporation of new genetic testing modalities to help guide a precision medicine approach. Additionally, we present a comprehensive literature summary on the most clinically relevant genomic aberrations in DLBCL, NOS. Based upon the survey results and literature review, we propose a standardized, tiered testing approach which will help laboratories optimize genomic testing in order to provide the maximum information to guide patient care.

Concordance of Peripheral Blood and Bone Marrow Next-Generation Sequencing in Hematologic Neoplasms.

Objective: Mutational analysis by next-generation sequencing (NGS) obtained by peripheral blood NGS has been of clinical interest to use as a minimally invasive screening tool. Our study evaluates the correlation between NGS results on peripheral blood and bone marrow in hematolymphoid disease. Method: We evaluated patients who had NGS for presumed hematologic malignancy performed on peripheral blood and bone marrow within a 1-year interval of each other. We excluded cases in which chemotherapy or bone marrow transplant occurred in the interval between the two tests. The concordance across peripheral blood and bone marrow NGS results was assessed by kappa coefficient analysis. Results: A total of 163 patients were studied. Concordance of peripheral blood and bone marrow NGS found in 150 patients (92.0%) with a kappa coefficient of 0.794 (kappa standard error 0.054) and P value for testing kappa <0.0001. Myeloid neoplasms showed concordant results in 77/78 cases (98.7%) with a kappa coefficient of 0.916. Lymphoid neoplasms showed concordant results in 26/31 cases (83.9%) with a kappa coefficient of 0.599. Nonneoplastic cases showed concordant results in 47/54 cases (87.0%) with a kappa coefficient of 0.743. Conclusion: Peripheral blood NGS is a reliable tool for mutational analysis and provides a less invasive method for screening and monitoring of the molecular profile.

Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges.

Focal amplifications (FA) can mediate targeted therapy resistance in cancer. Understanding the structure and dynamics of FAs is critical for designing treatments that overcome plasticity-mediated resistance. We developed a melanoma model of dual MAPK inhibitor (MAPKi) resistance that bears BRAFV600 amplifications through either extrachromosomal DNA (ecDNA)/double minutes (DM) or intrachromosomal homogenously staining regions (HSR). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs exhibit drug addiction-driven structural loss of BRAF amplicons upon dose reduction. FA mechanisms can couple with kinase domain duplications and alternative splicing to enhance resistance. Drug-responsive amplicon plasticity is observed in the clinic and can involve other MAPK pathway genes, such as RAF1 and NRAS. BRAF FA-mediated dual MAPKi-resistant cells are more sensitive to proferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi resistance beyond cases of dedifferentiation. SIGNIFICANCE: Understanding the structure and dynamics of oncogene amplifications is critical for overcoming tumor relapse. BRAF amplifications are highly plastic under MAPKi dosage challenges in melanoma, through involvement of de novo genomic alterations, even in the HSR mode. Moreover, BRAF FA-driven, dual MAPKi-resistant cells extend the spectrum of resistance-linked ferroptosis sensitivity. This article is highlighted in the In This Issue feature, p. 873.

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.

Identification of novel PIEZO1 variants using prenatal exome sequencing and correlation to ultrasound and autopsy findings of recurrent hydrops fetalis.

Nonimmune hydrops fetalis (NIHF) is a rare disorder with a high perinatal mortality of at least 50%. One cause of NIHF is generalized lymphatic dysplasia (GLD), a rare form of primary lymphedema of the extremities and systemic involvement including chylothoraces and pericardial effusions. An autosomal recessive form of GLD has been described, caused by variants in the PIEZO1 gene. It has been reported clinically to cause NIHF and childhood onset of facial and limb lymphedema, most of which were diagnosed postnatally. We present a case of a woman with recurrent pregnancies affected by NIHF because of novel compound heterozygous variants in the PIEZO1 gene diagnosed prenatally using exome sequencing (ES). Two variants in PIEZO1 (c.3206G>A and c.6208A>C) were identified that were inherited from the father and mother, and are predicted to cause a nonsense and missense change, respectively, in the PIEZO1 subunits. Ultrasound demonstrated severe bilateral pleural effusions, whole body edema and polyhydramnios. Histopathology revealed an increased number of lymphatic channels, many of which showed failure of luminal canalization. Sanger sequencing confirmed the same variants in a prior fetal demise. We provide phenotypic correlation with ultrasound and autopsy finding, review PIEZO1 variants as a cause of GLD and discuss the uses of prenatal ES to date.

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei.

Following DNA replication, sister chromatids must stay connected for the remainder of the cell cycle in order to ensure accurate segregation in the subsequent cell division. This important function involves an evolutionarily conserved protein complex known as cohesin; any loss of cohesin causes premature sister chromatid separation in mitosis. Here, we examined the role of cohesin in sister chromatid cohesion prior to mitosis, using fluorescence in situ hybridization (FISH) to assay the alignment of sister chromatids in interphase Drosophila cells. Surprisingly, we found that sister chromatid cohesion can be maintained in G2 with little to no cohesin. This capacity to maintain cohesion is widespread in Drosophila, unlike in other systems where a reduced dependence on cohesin for sister chromatid segregation has been observed only at specific chromosomal regions, such as the rDNA locus in budding yeast. Additionally, we show that condensin II antagonizes the alignment of sister chromatids in interphase, supporting a model wherein cohesin and condensin II oppose each other's functions in the alignment of sister chromatids. Finally, because the maternal and paternal homologs are paired in the somatic cells of Drosophila, and because condensin II has been shown to antagonize this pairing, we consider the possibility that condensin II-regulated mechanisms for aligning homologous chromosomes may also contribute to sister chromatid cohesion.

A case series of symptomatic ocular tuberculosis and the response to anti-tubercular therapy.

OBJECTIVE: To identify the clinical pattern of symptomatic ocular tuberculosis (OTB) and the outcome following antitubercular therapy (ATT) in an endemic setting. DESIGN: A descriptive case series. SETTING: Tuberculosis and ophthalmology clinics, Teaching Hospital, Kandy, Sri Lanka. METHOD: We followed up patients with OTB on standard six-month regimen of ATT, from January 2006 to December 2008. Serial opthalmological assessment were done at the beginning and end of therapy and in each clinic visit. Relevant investigations were performed. Objective improvement of visual acuity was considered the primary clinical outcome. RESULTS: Tuberculous uveitis was the commonest manifestation observed in eighteen of twenty-three patients with symptomatic OTB. Retinal vasculitis (2), episcleritis (1), optic neuritis (1) and an inflammatory scleral nodule (1) were observed in the rest. Seventeen had Mantoux positivity over 15mm. Out of the seventeen patients (age range 25-74 years; 9 males) who completed ATT, fifteen had poor pre-treatment visual acuity, which improved in nine. Keratic precipitates, anterior segment cells, flaring, vitritis and macular oedema had resolved in majority. In patients who deteriorated despite therapy, retinal vasculitis with vitreous haemorrhage (1) and branch vein occlusion (1), persistent macular oedema (2), choroidal scar (1) and optic atrophy (1) were noted. CONCLUSION: OTB may present with varying manifestations, of which uveitis is the commonest. Majority with symptomatic OTB had a highly positive Mantoux test. Favourable clinical outcome with ATT was seen in patients who presented with uncomplicated disease. Standard regimen of ATT did not appear to be effective in patients with complications.

Cataract in central Sri Lanka: prevalence and risk factors from the Kandy Eye Study.

PURPOSE: To estimate the prevalence of and risk factors for cataracts in the Kandy District of central Sri Lanka. METHODS: A population-based, cross-sectional ophthalmic survey of the inhabitants of rural villages in central Sri Lanka was conducted; 1375 individuals participated (79.9%; age > or = 40 years, average age 57) and 1318 (95.9%) had an examinable lens in at least one eye. Data collection included district, age, occupation, education level, smoking history, height, weight and dilated lens assessment using Lens Opacities Classification System III grading: nuclear (> or =4), cortical (> or =2) and posterior subcapsular (> or =2) cataracts. Aphakic and pseudophakic eyes were included as operated cataracts for statistical analysis. RESULTS: The prevalence of any cataract including operated eyes was 33.1% (95% Confidence Interval (CI), 22.4-43.7%): 26.0% cortical; 7.9% posterior sub-capsular and 4.5% nuclear cataracts. No significant association was found between cataract and gender, smoking or outdoor occupation. Low level of education (secondary or higher vs no education: Odds Ratio (OR) 0.6, CI 0.4-0.9, P = 0.04) and shorter stature were associated with a higher likelihood of any cataract (OR 1.7, CI 1.1-2.7, P = 0.02). CONCLUSIONS: The overall prevalence of cataract in central Sri Lanka is similar to that in other developing Asian regions except for the unusually low prevalence of nuclear cataract. Illiteracy and height appear to be significant predictors for cataract in this population and further investigation is required to explore their influence.

Prevalence and determinants of age-related macular degeneration in central Sri Lanka: the Kandy Eye Study.

AIMS: To determine the prevalence, associations and risk factors for age-related macular degeneration (ARMD) in central Sri Lanka. METHODS: The study was a population-based, cross-sectional survey of residents aged > or = 40 years in rural Sri Lanka. ARMD was assessed on dilated fundoscopy using the International Age-Related Maculopathy Epidemiology Study Group classification system. RESULTS: Of the 1721 subjects identified, 1375 participated (79.9%). Of the participants, 1013 were aged > or = 50 years (73.6%). The prevalence of any ARMD (adjusted for study design) was 4.72 (95% CI 2.22 to 7.20)% with 3.82 (95% CI 1.60 to 6.04)% early ARMD and 1.70 (95% CI 0.14 to 3.27)% late ARMD. Age (p<0.001) and Sinhalese ethnicity (p = 0.016) were significantly associated with ARMD. Men had a tendency toward a higher prevalence of ARMD than women, although this was not statistically significant (p = 0.081). Ocular risk factors such as cortical cataract (p = 0.024) and pseudophakia (p = 0.003) were associated with ARMD on the univariate but not multivariate analyses. Illiteracy and the identification of social supports were significantly associated with ARMD on univariate analyses. However, only social support was statistically significant after multivariate analysis (p = 0.024). CONCLUSIONS: Although the prevalence of ARMD is slightly lower in Sri Lanka than surrounding regions, it contributes to a higher proportion of visual impairment, including blindness. Risk factors include age and Sinhalese ethnicity.

Prevalence of exfoliation syndrome in central Sri Lanka: the Kandy Eye Study.

AIMS: To report the prevalence and correlates of exfoliation syndrome (XFS) in central, rural Sri Lanka. METHODS: A population-based, cross-sectional ophthalmic survey of inhabitants 40 years of age and over from villages in the Kandy District was conducted. Selection was randomised using a cluster sampling process. 1721 eligible participants were identified, 1375 participated. A detailed ophthalmic history and examination including ocular biometry was made of each participant. RESULTS: The prevalence of XFS was estimated to be 1.1% (95% CI 0.5 to 1.5%; 22 eyes). XFS was bilateral in eight subjects, unilateral in six subjects. Univariate analysis demonstrated a significant association between XFS and increasing age (p<0.001), increasing intraocular pressure (odds ratio 1.2; 95% CI 1.09 to 1.27; p<0.001), nuclear cataracts (odds ratio 1.92; 95% CI 1.47 to 2.51; p<0.001), visual impairment (odds ratio 9.72; 95% CI 3.01 to 31.44; p<0.001) and a history of hypertension (odds ratio 3.89; 95% CI 1.14 to 13.16; p = 0.030). CONCLUSION: XFS in this Sri Lankan population was associated with advanced age, raised intraocular pressure, nuclear cataracts, hypertension and visual impairment.