An uninformative NIPT as an early indicator of cri-du-chat due to a chromosomal 5;18 translocation-An atypical presentation of a rare cytogenetic phenomenon.

We present a patient with cri-du-chat syndrome secondary to a rare cytogenetic mechanism. Our patient was the product of a dichorionic diamniotic twin pregnancy initially flagged with soft markers on ultrasound and uninformative single-nucleotide polymorphism (SNP)-based noninvasive prenatal testing (NIPT) for chromosome 18. Subsequent NIPT using proprietary-targeted amplification methodology returned low risk for chromosomal aneuploidies 13, 18, and 21. Due to postnatal clinical findings, a clinical microarray and chromosomal karyotype confirmed cri-du-chat syndrome due to a de novo psu dic(5;18) (p15.2, p11.32). In this report we focus on these cytogenetic changes and discuss some of the current guidelines for prenatal microarray indications.

Dual diagnosis of trisomy 21 and lethal perinatal Gaucher disease as a cause of non-immune hydrops fetalis in a twin pregnancy for a consanguineous couple.

Non-immune hydrops is a prenatal finding which can occur due to an underlying genetic diagnosis such as common chromosomal aneuploidy (Trisomy 21, Turner syndrome etc.). It is extremely rare to have more than one genetic cause of hydrops fetalis in a single pregnancy. This report describes a dichorionic diamniotic pregnancy for a consanguineous couple where noninvasive prenatal testing was "high risk" for Trisomy 21. Family declined amniocentesis and opted for postnatal genetic testing. The pregnancy was later complicated with severe hydrops fetalis leading to demise for one of the twins, and a premature delivery of the other twin who had remarkable collodion not in keeping with Trisomy 21. Postnatal genetic investigations confirmed both Trisomy 21 and prenatal lethal Gaucher disease in the survivor twin. This case report highlights some of the prenatal diagnostic challenges for a consanguineous couple where a rare cause of fetal hydrops was concealed in a setting of a common chromosomal aneuploidy. The prompt postnatal diagnosis of perinatal lethal Gaucher disease, confirmed with undetectable glucocerebrosidase enzyme activity, assisted the family in the decision of providing palliative care for their infant who was quickly deteriorating. The importance of postnatal genetic evaluation and its impact on immediate patient management in an NICU setting is emphasized. This dual diagnosis was significant for the couple as it explained pervious pregnancy losses and has important future recurrence risk implications.

A novel MAP3K7 mutation in a child with cardiospondylocarpofacial syndrome and orofacial clefting.

Here we present the case of a patient with a novel de novo, likely pathogenic, heterozygous MAP3K7 variant (c.528dupT, p.G177WfsX5) causing cardiospondylocarpofacial syndrome (CSCFS). The variant, which falls in exon 6, is the first frameshift or non-sense mutation to be connected to CSCFS and presents with a phenotype that shares features with other MAP3K7-linked pathologies, including frontometaphyseal dysplasia 2 (FMD2) and the syndrome arising from an interstitial 6q15 deletions which envelop the gene. Other known mutations associated with CSCFS are plotted in black text (1,2,3).

Dual BRCA1 and BRCA2 pathogenic variants in an adolescent with syndromic intellectual disability.

Pathogenic variants in the BRCA1 and BRCA2 genes are associated with increased risk for breast and ovarian cancers. Concurrent mutations in both genes in the same individual are rare but pose specific challenges when identified, usually through multigene panel testing or infrequently from a genome-wide analysis, such as whole-exome sequencing (WES). We present a 15-year-old female patient with syndromic intellectual disability whose exome reanalysis identified secondary findings of pathogenic BRCA1 and BRCA2 variants, both inherited paternally. We discuss the significant challenges posed by this finding in genetic counseling and cancer risk management of an adolescent with nonverbal intellectual disability, as well as the impact on their family. This rare case highlights the potential increased diagnostic yield of whole exome sequencing reanalysis and the consequences of secondary medically actionable results in a pediatric patient.

Pitfalls in Genetic Testing for Consanguineous Pediatric Populations.

We describe the diagnostic odyssey of an eight-year-old female born to consanguineous parents. Our patient presented with global developmental delay, regression, microcephaly, spastic diplegia, and leukodystrophy confirmed on brain magnetic resonance imaging (MRI). She was found on whole exome sequencing (WES) to have dual genetic diagnoses. The first was a homozygous pathogenic HERC2 gene partial deletion of exons 43-45 that causes HERC2-related disorder. The second was a homozygous pathogenic variant (c.836 C > T, p.A279 V) in the SUMF1 gene responsible for multiple sulfatase deficiency. This case highlights some of the challenges in diagnosing consanguineous pediatric populations where standard genetic and metabolic testing may not provide answers. Our case further supports the recent American College of Medical Genetics and Genomics (ACMG) recommendation of WES as a first or second-tier test for patients with developmental delay, particularly in a population where the chances of dual diagnosis is high.

Genetic simulation for high-stakes conversations.

BACKGROUND: High-stakes conversations are frequent in Medical Genetics. News shared is often perceived as "bad" and can lead to patient hostility. Breaking bad news (BBN) is therefore a challenging clinical task for physicians and is often included as a foundational skill in medical education. The methods of teaching this skill are variable, with no widely accepted standard. We propose the use of simulation as a safe and effective training tool. APPROACH: Medical Genetics residents participated in a 4-week curriculum on BBN and de-escalating patient hostility and anger. The curriculum consisted of (1) a standardised patient simulation scenario requiring the disclosure of abnormal prenatal test result to a hostile patient, (2) coaching and feedback by genetic counsellors (GCs), (3) reflective exercises, and (4) workshops on de-escalation techniques. Trainees completed a postsimulation survey and postencounter reflection forms. Written comments on the survey and the reflections were analysed for themes. EVALUATION: Six junior and four senior residents participated in this curriculum innovation. Analysis of reflections revealed that simulation coupled with the genetic counsellor's (GC) timely feedback and reflection exercise were good education strategies for practicing BBN and de-escalation techniques in a challenging counselling situation. Most of the trainees felt that this teaching approach was successful and should be used for future training. IMPLICATIONS: Simulation can help prepare Medical Genetics trainees deliver difficult news and successfully de-escalate a hostile patient encounter. Consideration should be given to counselling and de-escalation simulations as a useful addition to standing curricula for Medical Genetics trainees.

OTX2 mutation associated with severe myopia in a Canadian family.

PURPOSE: To describe a case of high myopia in a pediatric patient with a mutation in the OTX2 gene and further characterize the diverse ocular phenotypes of heterozygous OTX2 mutations. PATIENT AND METHODS: We describe a three-year-old girl who presented at two months old with abnormal eye movements and suspected retinal dystrophy. Clinical exam and electroretinography (ERG) were conducted, and molecular next generation sequencing (NGS) with the Inherited Retinal Dystrophies panel was completed in our patient and offered to the family. RESULTS: Further examination revealed progressive high myopia in our patient and her mother, alongside diffuse retinal thinning and normal ERG. NGS identified a likely pathogenic variant in the OTX2 gene (c.235 G > A) that was maternal in origin. There were no extra-ocular concerns in our patient, and brain MRI was normal. CONCLUSIONS: While OTX2 mutations are known to cause retinopathy, this case presents a unique phenotype through a heterozygous missense variant (c.235 G > A) underlying high myopia in a three-generation family. This case further supports the role of OTX2 in ocular development and demonstrates the variable expressivity of OTX2 mutations. Genetic testing in families with high myopia may be useful in future surveillance and preparation for ocular and extra-ocular complications associated with OTX2-syndrome presentations.

Resolving severe oligohydramnios as an early prenatal presentation of renal coloboma syndrome-A report of two generations.

This report suggests that self-resolving oligohydramnios is an early sign of malfunctioning kidney in individuals with renal coloboma syndrome (RCS) and demonstrates how a genetic diagnosis can impact patient and fetal management as it outlines two generations of RCS.

Role of matrix metalloproteinase MMP-2, MMP-9 and tissue inhibitor of metalloproteinase (TIMP-1) in the clinical progression of pediatric acute lymphoblastic leukemia.

BACKGROUND: Matrix metalloproteinases (MMPs) play a crucial role in cancer progression and metastasis, however their role in pediatric Acute lymphoblastic leukemia (ALL) is still unrevealed. METHODS: The diagnostic, prognostic and predictive value of tissue inhibitor of metalloproteinase (TIMP-1), MMP-2, MMP-9 and CD34+CD38- cancer stem cells (CSCs) were assessed in bone marrow (BM) samples of 76 ALL children using Flow Cytometry analysis. RESULTS: There was a significant increase in TIMP-1 [1.52 (0.41-10) versus 0.91(0.6-1.12); respectively, p < 0.001], and CSCs CD34+CD38- [1 (0.03-18.6) versus 0.3 (0.01-1.1), p < 0.001] expression in ALL patients compared to controls. While there were no significant differences regarding MMP-2 and MMP-9 expression between the two groups. The sensitivity, specificity, area under curve (AUC) of MMP-2 were (80.3%, 53.3% and 0.568, p = 0.404), and of MMP-9 were (53.9%, 40% and 0.660, p = 0.053). While that of TIMP-1 were (78.9%, 100% and 0.892, p < 0.001), and that of CD34+CD38- CSCs were (78.9%, 73.3% and 0.855, p < 0.001). Increased TIMP-1 expression associated with the high-risk disease (p < 0.001). CD34+CD38- CSCs and MMP-2 overexpression associated with MRD at day-15, increased BM blast cell count at diagnosis and at day-15 (p < 0.05). TIMP-1 overexpression is associated with shorter DFS and OS rates (p = 0.009 and p = 0.048). Multivariate logistic regression analysis showed that both TIMP-1 [OR: 4.224, p = 0.046], and CD34+CD38- CSCs [OR: 6.873, p = 0.005] could be potential independent diagnostic factors for pediatric ALL. CONCLUSION: TIMP-1 and CD34+CD38- CSCs could be possible useful diagnostic markers for pediatric ALL. Also, TIMP-1 is a promising prognostic marker for poor outcome of the patients.

Aromatase deficiency in an Ontario Old Order Mennonite family.

OBJECTIVES: Aromatase deficiency is a rare autosomal recessive disease that results in the absence of aromatase. In females it presents with ambiguous genitalia and lack of secondary sexual characteristics during puberty. Aromatase deficiency is not attributed to any specific population, but it is more commonly seen in consanguineous parents. Herein, we report the first Old Order Mennonite family with that diagnosis. CASE PRESENTATION: Our proband is an Old Order Mennonite female born with ambiguous genitalia who was identified to carry novel homozygous variant in the CYP19A1 gene c.1304G>A (p. Arg435His). Her older brother was later confirmed with the same genetic diagnosis. CONCLUSIONS: Recognizing the cultural sensitivity, unrecognized affected cases, and late presentation of males affected with aromatase deficiency, this condition may be more prevalent than believed in that population.

The phenotypic spectrum of AMER1-related osteopathia striata with cranial sclerosis: The first Canadian cohort.

Osteopathia striata with cranial sclerosis (OSCS; OMIM# 300373) is a rare X-linked disorder caused by mutations of the AMER1 gene. OSCS is traditionally considered a skeletal dysplasia, characterized by cranial sclerosis and longitudinal striations in the long bone metaphyses. However, OSCS affects many body systems and varies significantly in phenotypic severity between individuals. This case series focuses on the phenotypic presentation and development of individuals with OSCS. We provide an account of 12 patients with OSCS, ranging from 5 months to 38 years of age. These patients were diagnosed with OSCS after genetic testing confirmed pathogenic mutations in AMER1. Patient consent was obtained for photos and participation. Data were collected regarding perinatal history, dysmorphic features, and review of systems. This case series documents common facial dysmorphology, as well as rare extraskeletal features of OSCS, including two patients with intestinal malrotation and two patients with pyloric stenosis. We share four apparently nonmosaic males with OSCS (one de novo and three maternal variants). We also provide a clinical update on a patient who was previously published by Chénier et al. (2012). American Journal of Medical Genetics Part A, 158, 2946-2952. More research is needed to investigate the links between genotype and phenotype and assess the long-term comorbidities and overall quality of life of individuals with OSCS.

Clinical and technical assessment of MedExome vs. NGS panels in patients with suspected genetic disorders in Southwestern Ontario.

The adaptation of a broad genomic sequencing approach in the clinical setting has been accompanied by considerations regarding the clinical utility, technical performance, and diagnostic yield compared to targeted genetic approaches. We have developed MedExome, an integrated framework for sequencing, variant calling (SNVs, Indels, and CNVs), and clinical assessment of ~4600 medically relevant genes. We compared the technical performance of MedExome with the whole-exome and targeted gene-panel sequencing, assessed the reasons for discordance, and evaluated the added clinical yield of MedExome in a cohort of unresolved subjects suspected of genetic disease. Our analysis showed that despite a higher average read depth in panels (3058 vs. 855), MedExome yielded full coverage of the enriched regions (>20X) and 99% variant concordance rate with panels. The discordance rate was associated with low-complexity regions, high-GC content, and low allele fractions, observed in both platforms. MedExome yielded full sensitivity in detecting clinically actionable variants, and the assessment of 138 patients with suspected genetic conditions resulted in 76 clinical reports (31 full [22.1%], 3 partial, and 42 uncertain/possible molecular diagnoses). MedExome sequencing has comparable performance in variant detection to gene panels. Added diagnostic yield justifies expanded implementation of broad genomic approaches in unresolved patients; however, cost-benefit and health systems impact warrants assessment.

TP63-mutation as a cause of prenatal lethal multicystic dysplastic kidneys.

BACKGROUND: Ectrodactyly-ectodermal dysplasia-clefting syndrome 3 (EEC) is one of the six overlapping syndromes caused by mutations in the tumor protein p63 gene (TP63). EEC is suspected when patients have cleft hands or feet, polydactyly, and syndactyly, abnormal development of the ectodermally derived structures, and orofacial clefting. Genitourinary (GU) anomalies have been identified in patients with EEC, yet these are often under-recognized and under-reported. The available literature on sonographic prenatal findings is sparse, especially when considering GU anomalies. METHODS: We present the case of a male stillborn fetus, who was found antenatally to have multicystic dysplastic kidneys and anhydramnios. Following the termination of pregnancy, examination and autopsy further revealed unilateral polydactyly and bilateral syndactyly which had not been previously identified on antenatal ultrasound. RESULTS: Whole-exome sequencing (WES) revealed a de novo heterozygous pathogenic variant in exon 5 of the TP63 gene: p.His247Arg: c.740A>G (NM_003722.4) which has been reported in the literature. The His247Arg variant has been published as a pathogenic variant in association with EEC, both with and without orofacial clefting. CONCLUSION: Our prenatal case expands the phenotypic spectrum of TP63-related disorders in general. In addition, it adds to the phenotype associated with the His247Arg pathogenic variant responsible for EEC. Further, we highlight the importance of WES as a postnatal tool to help clarify unexpected findings, and as a way to add to the spectrum of existing phenotypes of known single-gene disorders.

Diagnostic Utility of Genome-wide DNA Methylation Testing in Genetically Unsolved Individuals with Suspected Hereditary Conditions.

Conventional genetic testing of individuals with neurodevelopmental presentations and congenital anomalies (ND/CAs), i.e., the analysis of sequence and copy number variants, leaves a substantial proportion of them unexplained. Some of these cases have been shown to result from DNA methylation defects at a single locus (epi-variants), while others can exhibit syndrome-specific DNA methylation changes across multiple loci (epi-signatures). Here, we investigate the clinical diagnostic utility of genome-wide DNA methylation analysis of peripheral blood in unresolved ND/CAs. We generate a computational model enabling concurrent detection of 14 syndromes using DNA methylation data with full accuracy. We demonstrate the ability of this model in resolving 67 individuals with uncertain clinical diagnoses, some of whom had variants of unknown clinical significance (VUS) in the related genes. We show that the provisional diagnoses can be ruled out in many of the case subjects, some of whom are shown by our model to have other diseases initially not considered. By applying this model to a cohort of 965 ND/CA-affected subjects without a previous diagnostic assumption and a separate assessment of rare epi-variants in this cohort, we identify 15 case subjects with syndromic Mendelian disorders, 12 case subjects with imprinting and trinucleotide repeat expansion disorders, as well as 106 case subjects with rare epi-variants, a portion of which involved genes clinically or functionally linked to the subjects' phenotypes. This study demonstrates that genomic DNA methylation analysis can facilitate the molecular diagnosis of unresolved clinical cases and highlights the potential value of epigenomic testing in the routine clinical assessment of ND/CAs.

Challenges in Diagnosing Rare Genetic Causes of Common In Utero Presentations: Report of Two Patients with Mucolipidosis Type II (I-Cell Disease).

Traditional approaches to prenatal genetic diagnosis for common presentations such as short femurs or intrauterine growth restriction are imperfect, and whole-exome sequencing is an emerging option. Mucolipidosis type II (I-cell disease) is an ultra-rare autosomal recessive lysosomal storage disorder with the potential for prenatal-onset skeletal and placental manifestations. We describe the prenatal signs in two recent unrelated patients with confirmed diagnoses soon after birth. In both cases, parents were consanguineous but there was no known family history of mucolipidosis type II. False reassurance was provided after negative testing for another disease with overlapping prenatal manifestations already present in one of the families, emphasizing that offspring of consanguineous parents can be at risk for more than one recessive condition. Our experience illustrates the potential advantages in expanding prenatal applications of WES for the identification of rare single gene disorders in offspring of consanguineous unions.

Nonisolated diaphragmatic hernia in Simpson-Golabi-Behmel syndrome.

OBJECTIVE: Congenital diaphragmatic hernia (CDH) is associated with Simpson-Golabi-Behmel syndrome (SGBS), but few cases diagnosed prenatally have been reported. The aim of this series is to highlight the association of nonisolated CDH with SGBS type I on prenatal ultrasound and emphasize the importance of genetic testing, fetal autopsy, and family history in confirming this diagnosis. METHOD: Retrospective review of 3 cases of SGBS type I in a single tertiary care centre. Family history, fetal ultrasound, autopsy findings, and genetic testing for GPC3 was performed for each case. RESULTS: Fetal ultrasound findings in the second trimester were CDH, omphalocele, increased nuchal fold, renal anomaly, and cleft lip and palate. Fetal autopsy confirmed the prenatal ultrasound findings and also showed dysmorphic facial features and premalignant lesions on renal and gonadal histology. Microarray and DNA analysis of the GPC3 gene confirmed the diagnosis of SGBS type I in each case. CONCLUSION: Nonisolated CDH in a male fetus suggests a diagnosis of SGBS type I. Fetal autopsy, pedigree analysis, and genetic testing for GPC3 are all essential to confirming the diagnosis. The histological findings of ovotestes and nephroblastomatosis indicate that cancer predisposition is established early in fetal life.

Alagille syndrome: clinical perspectives.

Alagille syndrome is an autosomal dominant, complex multisystem disorder characterized by the presence of three out of five major clinical criteria: cholestasis with bile duct paucity on liver biopsy, congenital cardiac defects (with particular involvement of the pulmonary arteries), posterior embryotoxon in the eye, characteristic facial features, and butterfly vertebrae. Renal and vascular abnormalities can also occur. Inter- and intrafamilial variabilities in the clinical manifestations are common. We reviewed the clinical features and management as well as the molecular basis of Alagille syndrome.