Assessment of Factors Associated With the Evaluation of Children for Leukemia Predisposition Syndromes: A Retrospective Single-center Study.

Five to 10% of children with cancer are thought to have a cancer predisposition syndrome (CPS). Referral guidelines for leukemia predisposition syndromes are limited and vague, requiring the treating provider to determine whether patients should have a genetics evaluation. We evaluated referrals to the pediatric cancer predisposition clinic (CPP), the prevalence of CPS in those who elected to pursue germline genetic testing, and assessed for associations between a patient's medical history and the diagnosis of a CPS. Data were obtained via chart review of children diagnosed with leukemia or myelodysplastic syndrome between November 1, 2017, and November 30, 2021. A total of 22.7% of pediatric leukemia patients were referred for evaluation in the CPP. Of the participants evaluated with germline genetic testing, the prevalence of a CPS was 25%. Our study was able to find a CPS in different malignancies, including acute lymphoblastic leukemia, acute myeloid leukemia, and myelodysplastic syndrome. We did not find associations between a participant with an abnormal CBC before diagnosis or hematology visit and the diagnosis of a CPS. Our study supports that a genetic evaluation should be available to all children with leukemia as medical and family history alone is not predictors of a CPS.

Constitutional POLE variants causing a phenotype reminiscent of constitutional mismatch repair deficiency.

Heterozygous POLE or POLD1 germline pathogenic variants (PVs) cause polymerase proofreading associated polyposis (PPAP), a constitutional polymerase proofreading deficiency that typically presents with colorectal adenomas and carcinomas in adulthood. Constitutional mismatch-repair deficiency (CMMRD), caused by germline bi-allelic PVs affecting one of four MMR genes, results in a high propensity for the hematological, brain, intestinal tract, and other malignancies in childhood. Nonmalignant clinical features, such as skin pigmentation alterations, are found in nearly all CMMRD patients and are important diagnostic markers. Here, we excluded CMMRD in three cancer patients with highly suspect clinical phenotypes but identified in each a constitutional heterozygous POLE PV. These, and two additional POLE PVs identified in published CMMRD-like patients, have not previously been reported as germline PVs despite all being well-known somatic mutations in hyper-mutated tumors. Together, these five cases show that specific POLE PVs may have a stronger "mutator" effect than known PPAP-associated POLE PVs and may cause a CMMRD-like phenotype distinct from PPAP. The common underlying mechanism, that is, a constitutional replication error repair defect, and a similar tumor spectrum provide a good rationale for monitoring these patients with a severe constitutional polymerase proofreading deficiency according to protocols proposed for CMMRD.

Evaluation of barriers to referral for cancer predisposition syndromes in pediatric oncology patients in the United States.

Cancer predisposition syndromes (CPS) are underdiagnosed in the pediatric population, though the diagnosis of a CPS has important implications for the child and their family. CPS are often diagnosed by geneticists or oncologists with expertise in CPS following a malignancy. This requires a member of the care team, most commonly, the treating oncologist to suspect a CPS and refer the patient for CPS assessment. An online survey was distributed to members of the Children's Oncology Group to elucidate current referral practices and barriers to referral for patients suspected to have a CPS. Of the 183 respondents, 86.1% was pediatric oncologists and most (68.5%) used formal guidelines to aid in assessment. Most respondents indicated they would rarely refer patients with tumors highly associated with CPS for genetic assessment. Participants were more likely to refer patients with malignancy and additional features of a CPS than for a specific type of cancer, despite the use of guidelines. Parent knowledge of family history was considered the most challenging barrier to obtaining a family history, though a thorough pedigree was not consistently elicited. Providers indicated the most significant barrier to referral for CPS assessment was priority given the patient's immediate care needs. Identification of these barriers provides direction to focus efforts to increase referrals. Provider education about CPS, clear referral guidelines, and implementation of or increased collaboration with a genetic counselor in the pediatric oncology clinic may encourage CPS assessment and enable oncologists to focus on the patient's immediate care needs.

Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain.

PURPOSE: We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1ß subunit of the cyclic AMP-dependent protein kinase A (PKA). METHODS: Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development. RESULTS: Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs. CONCLUSION: Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.

Phenotypic expansion in KIF1A-related dominant disorders: A description of novel variants and review of published cases.

KIF1A is a molecular motor for membrane-bound cargo important to the development and survival of sensory neurons. KIF1A dysfunction has been associated with several Mendelian disorders with a spectrum of overlapping phenotypes, ranging from spastic paraplegia to intellectual disability. We present a novel pathogenic in-frame deletion in the KIF1A molecular motor domain inherited by two affected siblings from an unaffected mother with apparent germline mosaicism. We identified eight additional cases with heterozygous, pathogenic KIF1A variants ascertained from a local data lake. Our data provide evidence for the expansion of KIF1A-associated phenotypes to include hip subluxation and dystonia as well as phenotypes observed in only a single case: gelastic cataplexy, coxa valga, and double collecting system. We review the literature and suggest that KIF1A dysfunction is better understood as a single neuromuscular disorder with variable involvement of other organ systems than a set of discrete disorders converging at a single locus.

Chromosome 2q12.3-q13 copy number variants in patients with neurodevelopmental disorders: genotype-phenotype correlation and new hotspots.

INTRODUCTION: The complex structure of the chromosome 2q12.3-q13 region provides a high chance of recombination events between various low copy repeats (LCRs). Copy number variants (CNV) in this region are present in both healthy populations and individuals affected with developmental delay, autism and congenital anomalies. Variable expressivity, reduced penetrance and limited characterization of the affected genes have complicated the classification of the CNVs clinical significance. METHODS: Chromosomal microarray analysis data were reviewed for 10 298 patients with neurodevelopmental disorders referred to the UPMC Medical Genetics and Genomics Laboratories. A genotype-phenotype correlation was performed among the patients harboring the 2q12.3-q13 CNVs with overlapping genomic intervals. RESULTS: We identified 17 (1 in ~600) individuals with rare CNVs in the 2q12.3-q13 region, including nine patients with deletions, seven individuals with duplications and one patient who had both a deletion and a duplication. Likely pathogenic CNVs with the breakpoints between LCRs encompassing the potential dosage-sensitive genes BCL2L11, BUB1, FBLN7 and TMEM87B were the most common. CNVs were also observed between LCRs surrounding the RANBP2 and LIMS1 genes. CONCLUSION: Our study provides evidence for pathogenic CNV hotspots within the chromosome 2q12.3-q13 region. We suggest CNV classification based on the affected interval and the involvement of potential dosage-sensitive genes in these patients.

Influence of N-alkyl substituents and counterions on the structural and mesomorphic properties of guanidinium salts: experiment and quantum chemical calculations.

A series of N-4-(4'-alkoxybiphenyl)-N',N',N",N"-tetramethylguanidinium salts was synthesized with varying alkoxy chain lengths and additional N-alkyl substituents, each with a number of different counterions. X-ray crystal-structure analyses of 1b I, 1b PF(6), 2a I, and 4a I reveal bilayer structures in the solid state and, for the 1b and 1b PF(6) salts, a hydrogen-bond-type connectivity between the guanidinium N-H group and the anion is found. For the N-alkyl homologues 2a I and 4a I the anion is still oriented close to the head group, although at a larger distance. Ion pairs are present also in solution, as demonstrated by (1)H NMR: the N-H chemical shift shows a good linear correlation with the radius, and hence the hardness, of the anion. The intramolecular conformational flexibility of 1b I, 2b I, 3b I, and 4b I was studied by temperature-dependent (1)H NMR spectroscopy and discrete activation barriers were determined for rotations about each of the three C-N partial double bonds of the guanidinium core. The relative heights of the individual barriers change between the N-H and the N-alkylguanidinium salts. A fourth barrier is observed for the rotation about the N-biphenyl bond. DFT calculations of charge densities show that the positive charge resides primarily on the central carbon atom. Rotational barriers were calculated for N'-substituted 2-amino-1,3-dimethylimidazolidinium cations as models, and are in qualitatively good agreement with the NMR data. Mesomorphic properties were studied by differential-scanning calorimetry, polarizing optical microscopy, and X-ray diffraction (WAXS/SAXS). All liquid-crystalline guanidinium salts exhibit smectic A mesophases. Clearing temperatures show a linear correlation with the anionic radius. Substitution of the N-H group with methyl, ethyl, or propyl results in decreasing mesophase widths and a concomitant shrinkage of the layer spacings.

Autism spectrum disorder in females with ARHGEF9 alterations and a random pattern of X chromosome inactivation.

Proper function of GABAergic synapses depends upon the postsynaptic compartment anchoring of neurotransmitter receptors to the membrane by gephyrin and collybistin (Cb). In humans, Cb is encoded by ARHGEF9 on Xq11.1. ARHGEF9 alterations, some inherited from unaffected mothers, have been reported in males with autism, seizures and severe neurodevelopmental abnormalities. In females, a spectrum of mild to moderate phenotype has been detected. We report two unrelated females with autism and mild intellectual disability. High resolution X-chromosome microarray analysis revealed de novo intragenic deletions in ARHGEF9 of 24 kb and 56 kb involving exons 5-8 and exons 3-8 and leading to truncated forms of collybistin. Peripheral blood samples revealed random X-chromosome inactivation in both patients. To explain phenotypic variability in female patients, we propose a model for disruption of collybistin and various irregular interactions in post-synaptic neurons based on X inactivation patterns. Our findings highlight the importance of ARHGEF9 integrity and suggest further research on its correlation with autism and neurobehavioral problems.