Minimal Deletion Research Articles

Risk of meningomyelocele mediated by the common 22q11.2 deletion.

Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.

TAD boundary deletion causes PITX2-related cardiac electrical and structural defects

While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.

The value of minimal residual disease and IKZF1 deletion for predicting prognosis in adult patients with B-cell acute lymphoblastic leukemia

Objective: To reassess the prognostic value of minimal residual disease (MRD) and IKZF1 gene deletions in adults with B-cell acute lymphoblastic leukemia (B-ALL) who received pediatric-specific chemotherapy regimens during the Nanfang Hospital PDT-ALL-2016 trial. Methods: We retrospectively analyzed the prognosis of 149 adult patients with B-ALL who were admitted to Nanfang Hospital from January 2016 to September 2020. Prognostic factors were identified using Cox regression models. Results: The complete remission rate was 93.2% in 149 patients, with a 5-year overall survival (OS) rate of (54.3±5.0) % and a cumulative incidence of relapse (CIR) of (47.5±5.2) %. The Cox regression analysis revealed that MRD positivity at day 45 (MRD(3)) after induction therapy was independently associated with relapse risk (HR=2.535, 95%CI 1.122-5.728, P=0.025). Deletion of IKZF1 gene was independently associated with mortality risk (HR=1.869, 95%CI 1.034-3.379, P=0.039). Based on MRD(3) and IKZF1 gene status, we categorized adult patients with B-ALL into the low-risk (MRD(3)-negative and IKZF1 gene deletion-negative) and high-risk (MRD(3)-positive and/or IKZF1 gene wild type) groups. The 5-year OS and CIR rates were (45.5±6.0) % vs (69.4±8.6) % (P<0.001) and (61.6±8.3) % vs (25.5±6.5) % (P<0.001), respectively, in the high-risk and low-risk groups, respectively. The multivariate analysis showed that the high-risk group was an independent risk factor for OS (HR=3.937, 95%CI 1.975-7.850, P<0.001) and CIR (HR=4.037, 95%CI 2.095-7.778, P<0.001) . Conclusion: The combined use of MRD and IKZF1 gene in prognostic stratification can improve clinical outcome prediction in adult patients with B-ALL, helping to guide their treatment.

#152 : Exploring the Limitations of Linkage-Only PGT-M

Background and Aims: Although PGT-M cases can be conducted using linkage only, the inclusion of a direct test targeting the relevant genetic variants should be fundamental to best practise. We present four cases illustrating the limitations of linkage only PGT-M. Methods: Three cases used STRs for linkage analysis and the fourth Illumina Infinium Karyomapping. Direct variant detection encompassed Sanger sequencing, STRs and/or fragment PCR. Results: Case 1 Osteoporosis-pseudoglioma syndrome Sanger sequencing for LRP5c.3107G[Formula: see text]A and LRP5c.4487C[Formula: see text]A were critical for identifying a recombination in the familial control and subsequent correct assignment of STR phasing. Case 2 Osteogenesis imperfecta type I SNP-based linkage identified a recombinant embryo. Sanger sequencing for COL1A1c.2461G[Formula: see text]A resolved an unknown status to affected. Case 3 Neurofibromatosis type II Variant detection in this de novo mosaic case used two STRs within the NF2 exon2-11del to establish low- and high-risk linkage patterns. Two tumour samples with different second hit mutations exhibited reduced signal intensity for one allele. This was consistent with the presence of a weaker deleted allele due to sample contamination with non-tumour cells. Four of nine embryos contained two alleles within the minimum deletion and were first choice for transfer, resulting in an NAD prenatal confirmation and healthy liveborn. Case 4 Neurofibromatosis type I A de novo mosaic case required reverse linkage by means of a direct assay for the NF1c.1445_1446insCC variant. Affected embryos were subsequently used to phase flanking STRs and obtain linkage, resulting in one liveborn and one ongoing pregnancy. Conclusions: When a direct test is not included in PGT-M, a family may not be able to be offered a test, or misdiagnosis risk may increase. For de novo, mosaic and cases with suspected recombination in a reference sample, analysis of multiple cycles and/or the inclusion of non-clinical embryos to increase sample numbers improves accuracy of testing.

Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing

Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing.

Mitotic tethering enables inheritance of shattered micronuclear chromosomes.

Chromothripsis, the shattering and imperfect reassembly of one (or a few) chromosome(s)1, is an ubiquitous2 mutational process generating localized and complex chromosomal rearrangements that drive genome evolution in cancer. Chromothripsis can be initiated by mis-segregation errors in mitosis3,4 or DNA metabolism5-7 that lead to entrapment of chromosomes within micronuclei and their subsequent fragmentation in the next interphase or following mitotic entry6,8-10. Here we use inducible degrons to demonstrate that chromothriptically produced pieces of a micronucleated chromosome are tethered together in mitosis by a protein complex consisting of mediator of DNA damage checkpoint 1(MDC1), DNA topoisomerase II-binding protein 1(TOPBP1) and cellular inhibitor of PP2A (CIP2A), thereby enabling en masse segregation to the same daughter cell. Such tethering is shown to be crucial for the viability of cells undergoing chromosome mis-segregation and shattering after transient inactivation of the spindle assembly checkpoint. Transient, degron-induced reduction in CIP2A following chromosome micronucleation-dependent chromosome shattering is shown to drive acquisition of segmental deletions and inversions. Analyses of pancancer tumour genomes showed that expression of CIP2A and TOPBP1 was increased overallin cancers withgenomic rearrangements, including copy number-neutralchromothripsiswith minimal deletions, but comparatively reduced in cancers with canonical chromothripsis in which deletions were frequent. Thus, chromatin-bound tethers maintain the proximity of fragments of a shattered chromosome enabling their re-encapsulation into, and religation within, a daughter cell nucleus to form heritable, chromothriptically rearranged chromosomes found in the majority of human cancers.

Accurate Detection of Clinically Actionable Copy Number Variants in Diverse Hematological Neoplasms By Routine Targeted Sequencing: A Comparative Performance Study

Background: Accurate genotyping of Copy Number Variations (CNVs) is an essential part of the clinical evaluation of diverse hematologic malignancies. Conventional karyotyping and FISH are current gold standards to assess CNVs, but both have some limitations. Next-generation targeted sequencing panels are commonly incorporated into current clinical practice in most cancer centers. We examined the utility of CANARy (Copy number ANomaly Assessment and Recovery), a CNV profiling method for three hematological malignancies using targeted panel sequencing data. Patients and Methods: We studied patients with myelodysplastic syndrome (MDS), chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), and plasma cell disorders (PCD) identified from a cohort of 4752 hematological specimens profiled at Stanford University by conventional cytogenetics and next-generation sequencing (NGS) between 2018 and 2021. We curated a cohort of 200 patients diagnosed with MDS (n=72), CLL (n=46), and PCDs including MM, AL amyloidosis, and MGUS (PCD, n=82), along with 50 cytogenetically normal controls. Specimens were bone marrow aspirates, peripheral blood, or FFPE tissue. All samples were characterized by conventional metaphase karyotyping and/or FISH and we focused on the analysis of clinically relevant CNV (-5q, -7/-7q, -20q, +8 for MDS; -11q22, -13q14, -17p13, +12 for CLL; and +1q21, -1p32, -13q14, -17p.13 for PCD). The specimens separately had clinical NGS (164 genes, Heme-STAMP) performed no more than four weeks from standard cytogenetic analysis. We applied multiple CNV enumeration tools to sequencing data for CNV genotyping at these loci, including our recently developed method CANARy (Chabon et al, Nature 2020). CANARy is a read depth-based, genome-wide CNV caller from targeted sequencing data that combines information from on-target and off-target fragments to assign a final Z-score and copy number index to a set of pre-defined genomic regions. We benchmarked CANARy alongside three others publicly available CNV callers: CNVkit (Talevich et al, PLoS Comput Biol. 2016), ichorCNA (Adalsteinsson et al, Nat Commun. 2017), and WISECONDOR (Straver et al, Nucleic Acids Res. 2014). All tools were run using the default parameters and following author recommendations. We calculated the accuracy and other statistics parameters for each CNV caller, considering karyotype/FISH as the true reference. We estimated tumor fraction using two strategies: the variant allele fraction (VAF) of disease-related driver mutations and using the ichorCNA estimate. Results: A total of 211 CNVs were identified by karyotype and/or FISH, with disease-specific distribution summarized in Fig. A. CANARy detected 148/211 (70.1%), CNVkit 88/211 (41.7%), ichorCNA 116/211 (55%) and WISECONDOR 158/211 (74.9%). The overall accuracy for CANARy, CNVkit, ichorCNA and WISECONDOR was 86.3%, 81.8%, 84.3% and 83.1% respectively. CANARy had both the highest overall accuracy (86.3%) and overall F1-score (0.73) (Fig.B). WISECONDOR had the highest number of false positives (83 vs. CANARy = 48). Interestingly, all CNV tools performed better in MDS specimens, with 92% accuracy for CANARy in MDS samples, likely related to the higher neoplastic purity of these samples. The median ichorCNA tumor fraction estimates for MDS, CLL and PCD were 22% (0-99%), 14% (0-70%), and 7% (0-94%), respectively. In addition, CNV calling was inferior in PCD tumors than other tumor types. Within CLL, -11q22 and -13q14 lesions were more challenging to detect with any of the four methods, with CANARy sensitivity of 50% and 31.3% respectively, likely related to the smaller minimal deletion regions of these lesions. The 17p deletion in CLL cases, known for its poor prognostic impact, was best identified by CANARy; with a 100% sensitivity and a 97.6% specificity. The only non-concordant result for -17p was a false positive that was detected by all 4 NGS CNV genotypers but not FISH, possibly suggesting a false negative FISH result. Conclusions: CANARy accurately identifies clinically significant CNVs in common hematologic neoplasms and could thus serve as a complementary approach to the current cytogenetic evaluation. CANARy uses data already generated from targeted sequencing panels and therefore does not impose additional work or cost. Low tumor fraction could be a limitation for CNV calling. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Abstract 5821: Enhanced tumorigenesis in a novel miR-216a knockout/KPC mouse model of pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) originates from both ductal and acinar cells of the pancreas. The highly abundant and acinar cell-enriched miR-216a is reduced during in vitro acinar ductal metaplasia (ADM), throughout PanIN progression, during the development of pancreatitis in mice and humans, and during development of mouse and human PDAC. To investigate the contribution of miR-216a in the development of PDAC, we generated a miR-216a germline knockout mouse (216aKO) via CRISPR genetic editing of a minimal and precise deletion of the miR-216a precursor sequence without affecting the host gene. We crossed this 216aKO mouse to the LSL-KrasG12D; LSL-Trp53Flox/+; Pdx1Cre/+ (KPC) mice to produce a transgenic mouse with an activating Kras mutation, p53 deletion, and knockout of miR-216a (referred to here as miR216aKPC). miR216aKPC displayed an increase in tumor progression compared to KPC and had reduced survival - median 15 weeks miR216aKPC vs. 25 weeks for KPC. miR216aKPC produced lung metastasis by 12 weeks of age which were not present in the lungs of similarly aged KPC mice. Transfection of miR-216a mimetic oligo into cell lines derived from KPC or 216aKPC mice did not reduce viability or alter cellular morphology, suggesting that a potential tumor suppressive role of miR-216a functions during the early stages of PDAC development. A three dimensional ADM assay using acinar cells derived from both mouse and human pancreata will be applied to investigate the contributions of miR-216a on the development of ADM and cell polarity. To discover miR-216a target genes that are responsible for the increased tumorigenesis, cell lines derived from miR216aKPC will be transfected with miR-216a mimetic or scrambled control oligo followed by RNA sequencing. Our results thus far suggest a tumor suppressive role for miR-216a in the early development of PDAC and future studies will investigate molecular and cellular mechanisms driving acinar cell-induced PDAC. Citation Format: Andrew A. Brock, Katherine Powell, Thomas D. Schmittgen, Lorenzo F. Sempere. Enhanced tumorigenesis in a novel miR-216a knockout/KPC mouse model of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5821.

Egyptian female with 8q22.2q22.3 microdeletion syndrome

8q22.2q22.3 microdeletion syndrome is a rare chromosomal anomaly that was first described 11 years ago. Main symptoms of this condition include delayed development, autism, epilepsy and characteristic facial features. Up to date, only eight cases with interstitial heterozygous deletions at 8q22.2q22.3 have been previously reported. Here, we reported a new patient from Egypt representing the first documented case in Africa and Middle East. Furthermore, we compared the clinical and molecular findings of all patients. All subjects differed in the deletion size and breakpoints with a minimal deletion overlap of 0.43 Mb containing at least 14 OMIM genes. The molecular profile of the reported cases may denote that the disease phenotype is mainly assigned by haploinsufficiency of several cognate genes, rather than deletion of specific genes as separate entities.

Molecular and phenotypic characteristics of 15q24 microdeletion in pediatric patients with developmental disorders

Chromosome 15q24 microdeletion is a rare genetic disorder characterized by development delay, facial dysmorphism, congenital malformations, and occasional autism spectrum disorder (ASD). In this study, we identified five cases of 15q24 microdeletion using multiplex ligation-dependent probe amplification (MLPA) technology in a cohort of patients with developmental delay and/or intellectual disability. Two of these five cases had deletions that overlapped with the previously defined 1.1 Mb region observed in most reported cases. Two cases had smaller deletions (< 0.57 Mb) in the 15q24.1 low copy repeat (LCR) B-C region. They presented significant neurobehavioral features, suggesting that this smaller interval is critical for core phenotypes of 15q24 microdeletion syndrome. One case had minimal homozygous deletion of less than 0.11 Mb in the 15q24.1 LCR B-C region, which contained CYP1A1 (cytochrome P450 family 1 subfamily A member 1) and EDC3 (enhancer of mRNA decapping 3) genes, resulting in poor immunity, severe laryngeal stridor, and lower limbs swelling. This study provides additional evidence of 15q24 microdeletion syndrome with genetic and clinical findings. The results will be of significance to pediatricians in their daily practice.

Minimal residual disease, long-term outcome, and IKZF1 deletions in children and adolescents with Down syndrome and acute lymphocytic leukaemia: a matched cohort study

SummaryBackgroundPatients with Down syndrome and acute lymphocytic leukaemia are at an increased risk of treatment-related mortality and relapse, which is influenced by unfavourable genetic aberrations (eg, IKZF1 deletion). We aimed to investigate the potential underlying effect of Down syndrome versus the effects of adverse cancer genetics on clinical outcome.MethodPatients (aged 1–23 years) with Down syndrome and acute lymphocytic leukaemia and matched non-Down syndrome patients with acute lymphocytic leukaemia (matched controls) from eight trials (DCOG ALL10 and ALL11, ANZCHOG ALL8, AIEOP-BFM ALL2009, UKALL2003, NOPHO ALL2008, CoALL 07-03, and CoALL 08-09) done between 2002 and 2018 across various countries (the Netherlands, the UK, Australia, Denmark, Finland, Iceland, Norway, Sweden, and Germany) were included. Participants were matched (1:3) for clinical risk factors and genetics, including IKZF1 deletion. The primary endpoint was the comparison of MRD levels (absolute MRD levels were categorised into two groups, low [<0·0001] and high [≥0·0001]) between patients with Down syndrome and acute lymphocytic leukaemia and matched controls, and the secondary outcomes were comparison of long-term outcomes (event-free survival, overall survival, relapse, and treatment-related mortality [TRM]) between patients with Down syndrome and acute lymphocytic leukaemia and matched controls. Two matched cohorts were formed: for MRD analyses and for long-term outcome analyses. For both cohorts, matching was based on induction regimen; for the long-term outcome cohort, matching also included MRD-guided treatment group. We used mixed-effect models, Cox models, and competing risk for statistical analyses.FindingsOf 251 children and adolescents with Down syndrome and acute lymphocytic leukaemia, 136 were eligible for analyses and matched to 407 (of 8426) non-Down syndrome patients with acute lymphocytic leukaemia (matched controls). 113 patients with Down syndrome and acute lymphocytic leukaemia were excluded from matching in accordance with predefined rules, no match was available for two patients with Down syndrome and acute lymphocytic leukaemia. The proportion of patients with high MRD at the end of induction treatment was similar for patients with Down syndrome and acute lymphocytic leukaemia (52 [38%] of 136) and matched controls (157 [39%] of 403; OR 0·97 [95% CI 0·64–1·46]; p=0·88). Patients with Down syndrome and acute lymphocytic leukaemia had a higher relapse risk than did matched controls in the IKZF1 deleted group (relapse at 5 years 37·1% [17·1–57·2] vs 13·2% [6·1–23·1]; cause-specific hazard ratio [HRcs] 4·3 [1·6–11·0]; p=0·0028), but not in the IKZF1 wild-type group (relapse at 5 years 5·8% [2·1–12·2] vs 8·1% [5·1–12·0]; HRcs 1·0 [0·5–2·1]; p=0·99). In addition to increased induction deaths (15 [6%] of 251 vs 69 [0·8%] of 8426), Down syndrome and acute lymphocytic leukaemia was associated with a higher risk of post-induction TRM compared with matched controls (TRM at 5 years 12·2% [7·0–18·9] vs 2·7% [1·3–4·9]; HRcs 5·0 [2·3–10·8]; p<0·0001).InterpretationInduction treatment is equivalently effective for patients with Down syndrome and acute lymphocytic leukaemia and for matched patients without Down syndrome. Down syndrome itself provides an additional risk in individuals with IKZF1 deletions, suggesting an interplay between the germline environment and this poor risk somatic aberration. Different treatment strategies are warranted considering both inherent risk of relapse and high risk of TRM.FundingStichting Kinder Oncologisch Centrum Rotterdam and the Princess Máxima Center Foundation, NHMRC Australia, The Cancer Council NSW, Tour de Cure, Blood Cancer UK, UK Medical Research Council, Children with Cancer, Swedish Society for Pediatric Cancer, Swedish Childhood Cancer Fund, Danish Cancer Society and the Danish Childhood Cancer Foundation.

UBA2 variants underlie a recognizable syndrome with variable aplasia cutis congenita and ectrodactyly

PurposeThe human chromosome 19q13.11 deletion syndrome is associated with a variable phenotype that includes aplasia cutis congenita (ACC) and ectrodactyly as specific features. UBA2 (ubiquitin-like modifier-activating enzyme 2) lies adjacent to the minimal deletion overlap region. We aimed to define the UBA2-related phenotypic spectrum in humans and zebrafish due to sequence variants and to establish the mechanism of disease. MethodsExome sequencing was used to detect UBA2 sequence variants in 16 subjects in 7 unrelated families. uba2 loss of function was modeled in zebrafish. Effects of human missense variants were assessed in zebrafish rescue experiments. ResultsSeven human UBA2 loss-of-function and missense sequence variants were detected. UBA2-phenotypes included ACC, ectrodactyly, neurodevelopmental abnormalities, ectodermal, skeletal, craniofacial, cardiac, renal, and genital anomalies. uba2 was expressed in zebrafish eye, brain, and pectoral fins; uba2-null fish showed deficient growth, microcephaly, microphthalmia, mandibular hypoplasia, and abnormal fins. uba2-mRNAs with human missense variants failed to rescue nullizygous zebrafish phenotypes. ConclusionUBA2 variants cause a recognizable syndrome with a wide phenotypic spectrum. Our data suggest that loss of UBA2 function underlies the human UBA2 monogenic disorder and highlights the importance of SUMOylation in the development of affected tissues.

Rapid Production of Multifunctional Self-Assembling Peptides for Incorporation and Visualization within Hydrogel Biomaterials.

Peptides are of continued interest for therapeutic applications, from soluble and immobilized ligands that promote desired binding or uptake to self-assembled supramolecular structures that serve as scaffolds in vitro and in vivo. These applications require efficient and scalable synthetic approaches because of the large amounts of material that often are needed for studies of bulk material properties and their translation. In this work, we establish new methods for the synthesis, purification, and visualization of assembling peptides, with a focus on multifunctional collagen mimetic peptides (mfCMPs) relevant for formation and integration within hydrogel-based biomaterials. First, a methodical approach useful for the microwave-assisted synthesis of assembling peptide sequences prone to deletions was established, beginning with the identification of the deleted residues and their locations and followed by targeted use of dual chemistry couplings for those specific residues. Second, purification techniques that integrate the principles of heating and ion displacement with traditional chromatography and dialysis were implemented to improve separation and isolation of the desired multifunctional peptide product, which contained blocks for thermoresponsiveness and ionic interactions. Third, an approach for fluorescent labeling of these mfCMPs, which is orthogonal to their assembly and their covalent incorporation into a bulk hydrogel material, was established, allowing visualization of the resulting hierarchical fibrillar structures in three dimensions within hydrogels using confocal microscopy. The methods presented in this work allow the production of multifunctional peptides in scalable quantities and with minimal deletions, enabling future studies for better understanding of composition-structure-property relationships and for translating these biomaterials into a range of applications. Although mfCMPs are the focus of this work, the methods demonstrated could prove useful for other assembling peptide systems and for the production of peptides more broadly for therapeutic applications.

The Development and Application of a Base Editor in Biomedicine.

Using a base editor to generate monogenic disease models and correct pathogenic point mutations is a breakthrough technology for exploration and treatment of human diseases. As a burgeoning approach for genomic modification, the fused CRISPR/Cas9 with various deaminase separately has significantly increased the efficiency of producing a precise point mutation with minimal insertions or deletions (indels). Along with the flexibility and efficiency, a base editor has been widely used in many fields. This review discusses the recent development of a base editor, including evolution and advance, and highlights the applications and challenges in the field of gene therapy. Depending on rapid improvement and optimization of gene editing technology, the prospect of base editor is immeasurable.

Topic Maintenance and Topic Transition in a Couple’s Dinnertime Conversation

This paper investigates the patterns of topic maintenance and topic transition used to create conversation and their accompanying structural features speakers employ to signal these two conversational phenomena. The data are a 21-minute dyadic dinnertime conversation between a boyfriend and girlfriend; they are both native speakers of American English, in their late twenties. The two significant findings of the study are as follows. First, the data reveal that the speakers used three major techniques, namely minimal responses, substitutions, and deletions, to maintain the same topic of the conversation (Goffman, 1983; Radford &amp;amp; Tarplee, 2000; Abu Akel, 2002; Sukrutrit, 2010; Jeon, 2012). Second, in the analysis of topic transition, the data show that the speakers resorted to different types of topic transitions (i.e., collaborative, unilateral, linked, minimally linked, and sudden) to end an ongoing topic and start a new one (West &amp;amp; Garcia, 1988; Ainsworth-Vaughn, 1992; Okamoto &amp;amp; Smith-Lovin, 2001; Sukrutrit, 2010; Jeon, 2012).

A Brazilian cohort of individuals with Phelan-McDermid syndrome: genotype-phenotype correlation and identification of an atypical case

BackgroundPhelan-McDermid syndrome (PMS) is a rare genetic disorder characterized by global developmental delay, intellectual disability (ID), autism spectrum disorder (ASD), and mild dysmorphisms associated with several comorbidities caused by SHANK3 loss-of-function mutations. Although SHANK3 haploinsufficiency has been associated with the major neurological symptoms of PMS, it cannot explain the clinical variability seen among individuals. Our goals were to characterize a Brazilian cohort of PMS individuals, explore the genotype-phenotype correlation underlying this syndrome, and describe an atypical individual with mild phenotype.MethodologyA total of 34 PMS individuals were clinically and genetically evaluated. Data were obtained by a questionnaire answered by parents, and dysmorphic features were assessed via photographic evaluation. We analyzed 22q13.3 deletions and other potentially pathogenic copy number variants (CNVs) and also performed genotype-phenotype correlation analysis to determine whether comorbidities, speech status, and ASD correlate to deletion size. Finally, a Brazilian cohort of 829 ASD individuals and another independent cohort of 2297 ID individuals was used to determine the frequency of PMS in these disorders.ResultsOur data showed that 21% (6/29) of the PMS individuals presented an additional rare CNV, which may contribute to clinical variability in PMS. Increased pain tolerance (80%), hypotonia (85%), and sparse eyebrows (80%) were prominent clinical features. An atypical case diagnosed with PMS at 18 years old and IQ within the normal range is here described. Among Brazilian ASD or ID individuals referred to CNV analyses, the frequency of 22q13.3 deletion was 0.6% (5/829) and 0.61% (15/2297), respectively. Finally, renal abnormalities, lymphedema, and language impairment were found to be positively associated with deletion sizes, and the minimum deletion to cause these abnormalities is here suggested.ConclusionsThis is the first work describing a cohort of Brazilian individuals with PMS. Our results confirm the impact of 22q13 deletions on ASD and several comorbidities, such as hypotonia. The estimation of a minimal deletion size for developing lymphedema and renal problem can assist prediction of prognosis in PMS individuals, particularly those diagnosed in early infancy. We also identified one atypical individual carrying SHANK3 deletion, suggesting that resilience to such mutations occurs. This case expands the clinical spectrum of variability in PMS and opens perspectives to identify protective mechanisms that can minimize the severity of this condition.

On measures of nonplanarity of cubic graphs

We study two measures of nonplanarity of cubic graphs G, the genus γ (G), and the edge deletion number ed(G). For cubic graphs of small orders these parameters are compared with another measure of nonplanarity, the rectilinear crossing number (G). We introduce operations of connected sum, specified for cubic graphs G, and show that under certain conditions the parameters γ(G) and ed(G) are additive (subadditive) with respect to them.The minimal genus graphs (i.e. the cubic graphs of minimum order with given value of genus γ) and the minimal edge deletion graphs (i.e. cubic graphs of minimum order with given value of edge deletion number ed) are introduced and studied. We provide upper bounds for the order of minimal genus and minimal edge deletion graphs.

Abstract PR01: Distinct genomic alterations in prostate cancer of African American men

Abstract Background: Emerging observations highlight distinct biology of prostate cancer (CaP) among men of different ethnicities and races. Studies including reports from our institute have demonstrated remarkable ethnic/racial differences in the frequency of ERG oncogenic activation, one of the most common and widely studied CaP driver genes. Similarly, deletion of the PTEN tumor suppressor gene, an established cancer driver gene alteration, was shown to be more prevalent among men of European ancestry. We have reported the cumulative analyses of 435 patients (whole-genome sequencing [WGS]: 14, FISH evaluations: 101, SNP array: 320) comparing CaP genomes of African American and Caucasian American patients. An AA CaP genome associated minimum deletion site on 3q13.31 was identified by WGS and mapped to the Limbic System-Associated Membrane Protein (LSAMP) gene locus using the TCGA SNP array data of 44 AA and 260 CA tumors. Further, we also noted the AA CaP genome association of the Chromodomain Helicase DNA Binding Protein 1(CHD1) gene deletion. Methods: The frequency and prognostic associations of LSAMP, CHD1, and PTEN deletions was evaluated by FISH analyses in prostate tumor tissue microarray (TMA) with up to 20 years of follow-up. The TMA represented normal and tumor foci (1000+ cores) sampled by 2-3 cores including the spectrum of cell morphology and tumor pathology in matched cohort of 42 AA and 59 CA patients. ERG was evaluated in the same TMA by immunohistochemistry. Evaluation of ERG was extended to the assessment of whole mounted prostate sections of 336 AA and 594 CA patients from the equal-access military health care system, in which disparities in socioeconomic status, health awareness, and physical activity are minimized. Results: AA CaP genome-associated recurrent deletions of LSAMP (26% AA vs. 7% CA, p=0.006) and CHD1 (29% AA vs. 10% CA p=0.017) genes were identified. AA CaP patients harboring these genomic deletions in their CaP showed significantly higher risk of rapid disease progression as measured by biochemical recurrence. Consistent with previous reports, we noted significantly lower frequency of PTEN deletions (15% AA vs. 63% CA) and ERG expression (26% AA vs. 64%) in prostate cancers among AA men. In-depth evaluation of ERG frequencies in the context of multifocal disease provided definitive evidence for the difference in the frequency of ERG between AA (23%) and CA (49%) patients from the equal-access military health care system. Conclusions: Our study underscores that the biology of CaP has to be taken into consideration when new diagnostic and prognostic markers and therapeutic approaches are being developed in order to realize the true potential of precision medicine for all cancer patients. Note: This abstract was not presented at the conference. Citation Format: Albert Dobi, Gyorgy Petrovics, Hua Li, Denise Young, Yongmei Chen, Jacob Kagan, Sudhir Srivastava, Reinhard Ebner, Inger L. Rosner, Jennifer Cullen, Matthew L. Freedman, Isabell A. Sesterhenn, Zoltan Szallasi, Shiv Srivastava. Distinct genomic alterations in prostate cancer of African American men [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr PR01.

Hypothalamic loss of Snord116 recapitulates the hyperphagia of Prader-Willi syndrome.

Profound hyperphagia is a major disabling feature of Prader-Willi syndrome (PWS). Characterization of the mechanisms that underlie PWS-associated hyperphagia has been slowed by the paucity of animal models with increased food intake or obesity. Mice with a microdeletion encompassing the Snord116 cluster of noncoding RNAs encoded within the Prader-Willi minimal deletion critical region have previously been reported to show growth retardation and hyperphagia. Here, consistent with previous reports, we observed growth retardation in Snord116+/–P mice with a congenital paternal Snord116 deletion. However, these mice neither displayed increased food intake nor had reduced hypothalamic expression of the proprotein convertase 1 gene PCSK1 or its upstream regulator NHLH2, which have recently been suggested to be key mediators of PWS pathogenesis. Specifically, we disrupted Snord116 expression in the mediobasal hypothalamus in Snord116fl mice via bilateral stereotaxic injections of a Cre-expressing adeno-associated virus (AAV). While the Cre-injected mice had no change in measured energy expenditure, they became hyperphagic between 9 and 10 weeks after injection, with a subset of animals developing marked obesity. In conclusion, we show that selective disruption of Snord116 expression in the mediobasal hypothalamus models the hyperphagia of PWS.

Clinical features and gene mutation analysis of patients with Niemann-Pick disease type C

Objective: To analyze the clinical manifestations, therapeutic efficacy, prognosis and characteristics of NPC1 mutation in Chinese patients with Niemann-Pick disease type C(NPC). Methods: Ten unrelated Chinese NPC patients were diagnosed by NPC1 mutation analysis from July 2013 to February 2017 in Beijing Tian Tan Hospital of Capital Medical University. Clinical data of 10 cases were analyzed retrospectively which included clinical manifestations, laboratory results and NPC1 gene mutation features, and a series of follow-up were carried out about therapeutic efficacy and prognosis. Results: Ten patients suffering from NPC included 5 males and 5 females, aged from 42 days to 14 years when they presented to Tian Tan Hospital. According to their age of neurological onset, 4 were in early infantile period, 2 in late infantile period, 2 in juvenile periods, and the other 2 cases in neonatal period. They all presented with splenomegaly, 5 of 10 accompanied with hepatomegaly. Two cases of neonatal subtype presented mainly with delayed neonatal cholestatic jaundice and hepatosplenomegaly, accompanied with decreased muscle tone and slight psychomotor retardation. The other 8 cases presented with severe neurological involvement, such as progressive encephalopathy, ataxia and language impairment, 4 with dystonia, 3 with decreased muscle tension, 5 with vertical supranuclear gaze palsy, 5 with gelastic cataplexy, and 4 with epilepsy. Eight of 9 cases presented with foam cells in their bone marrow. Head MRI showed diffuse cerebral atrophy in 8 cases, thin corpus callosum in 2 cases, and brain white matter abnormal signals in 2 cases. Among 10 cases, 18 different mutations of NPC1 allelic genes were identified including 11 reported mutations, 3 novel missense mutations: c. 3683T>C (p.Met1128Thr), c.1926G>C (p.Met642Iie) and c. 3006C>G (p.Phe1002Leu), 2 novel nonsense mutation: c. 1142G>A(p.Trp381Ter ) and c. 3229C>T(p.Arg1077Ter), 1 novel minimal deletion mutation: c. 1385-1386del, and 1 novel intron mutation: c. 1757+ 5G>A. In 5 cases, the symptom of gelastic cataplexy was alleviated by imipramine, and the convulsion was relieved by valproate in 2 cases, by carbamazepine in 1 case at the beginning of seizure. During the 25 (3-66) months of follow-up, 4 cases died, the others' neurological symptoms were deteriorated progressively. Conclusions: The NPC1 gene mutation were high heterozygous in this group, and 7 novel mutations enriched the gene mutation spectrum of NPC1. The neurological manifestations were complicated in patients with NPC, and the symptomatology would be different according to their onset age of neurological symptoms. There might be effective symptomatic treatment for gelastic cataplexy by imipramine and for convulsion by valproate or carbamazepine.