Intronic Deletion Research Articles

Prenatal diagnosis of partial deletion of NRXN1 gene with combined CNV-seq and qPCR assays

To summarize the genetic diagnosis, low-depth copy number variation sequencing (CNV-seq) and prenatal finding in 7 fetuses with 2p16.3 deletions only involving the NRXN1 gene. The 7 fetuses have all been found to have loss of heterozygosity at 2p16.3 by CNV-seq, which were verified by quantitative real-time PCR (qPCR). Specific regions of NRXN1 gene deletions were identified, and the CNVs were verified in their parents. Outcome of the pregnancies were followed up. Among 16 502 prenatal samples, 7 fetuses were found to harbor a 120 kb ~ 900 kb microdeletion in the 2p16.3 region, which yielded a prevalence of 0.424‰. The deleted region mainly involved 50 200 000-51 880 000 positions of chromosome 2 and involved only the NRXN1 gene. All of the 7 fetal CNVs were confirmed by qPCR, including 2 cases with heterozygous deletion of exons 1 to 6, 1 with heterozygous deletion of exons 1 to 19, 1 with heterozygous deletion of exons 19 to 22, and 3 with heterozygous deletion of introns 6 to 7 of the NRXN1 gene. Verification in the parents had found that one deletion was inherited from the father, 1 was from the mother, 2 cases were de novo in origin, whilst the remaining 3 had refused parental verification. After genetic counseling, one couple had elected induced abortion, 1 case has not been born yet, whilst the other 5 cases were born healthy. Follow up had identified no mental abnormalities among the children. Seven fetuses with heterozygous 2p16.3 deletions only involving the NRXN1 gene were detected by CNV-seq. The specific deletion of the NRXN1 gene was verified by qPCR. Prenatal genetic counseling and fertility guidance has been provided to the particular family by combining the results of CNV testing, pedigree analysis and pregnancy outcome.

RF13 | PMON133 A novel variant in an intron consensus sequence associated with familial growth hormone deficiency

Abstract Splicing variants in the exon-intron boundaries of the GH1 gene have been reported to cause autosomal dominant growth hormone deficiency (GHD type 2). However, whether variants in the intron consensus sequence (XGGG repeats) have an important role in GH1 gene splicing has not been established. Two siblings (proband 1 and 2) were diagnosed with growth hormone deficiency due to poor linear growth at age 4 years (height SDS -2.2 and – 1.6, respectively). Peak serum GH levels with provocative testing were 4.39 ng/ml and 2.77 ng/ml, respectively. They had no other pituitary hormone deficiencies and their pituitary MRIs were normal. Both children are being treated with recombinant human GH (rhGH) with excellent responses in linear growth. Their mother also had a history of GHD in childhood and received rhGH from ages 4 to 13 years. After GH treatment, she reached a normal adult height. The remainder of her pituitary function was normal. Exome sequencing was performed on the probands, their affected mother, and unaffected maternal grandparents to identify the underlying genetic cause. Exome sequencing revealed that the affected mother carried a de novo variant in intron 3 of the GH1 gene (c.291+34G>A, NM_000515.5), and the intronic variant was passed on to the two probands. The variant is not found in the general population according to gnomAD. No other variants in GH1 or other genes were detected to cosegregate with GHD in this family. The intronic variant was located in one of the two intron consensus regions in intron 3 and was predicted by ESEfinder to create a new splicing enhancer (SF2/ASF) binding site. Because intron consensus sequence repeats are important for spliceosome assembly, the variant is predicted to cause aberrant pre-mRNA splicing but not affecting the donor or acceptor site. Previously, a variant in the intron consensus sequence, c.291+28G>A, was found to cause exon 3 skipping, presumably generating a small amount of 22 kDa GH but a large amount of 17 kDa GH. Small deletions in intron 3 (c.291+28_45del and c.291+56_77del) have also been reported to cause exon 3 skipping, categorized as GHD type 2. In vitro studies with the new variant will be required to confirm exon 3 skipping as the mechanism of GHD in this family. This novel intronic variant which creates a new splicing enhancer-binding site supports the previous finding that the intron consensus sequence plays a significant role in the splicing of GH1 pre-mRNA and results in autosomal dominant GHD. As other variants in intron consensus sequence sites may cause GHD type 2, we recommend genetic testing in patients with GHD include the intron consensus sequence regions. Presentation: Sunday, June 12, 2022 12:48 p.m. - 12:53 p.m., Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.

Genome-wide detection of human variants that disrupt intronic branchpoints.

Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of STAT2 in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of ITPKB in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from https://hgidsoft.rockefeller.edu/BPHunter and https://github.com/casanova-lab/BPHunter.

Copy-number variants in the contactin-5 gene are a potential risk factor for autism spectrum disorder

BackgroundContactin-5 (CNTN5) is a candidate risk gene for autism spectrum disorder (ASD). Previous attempts to associate CNTN5 CNVs with ASD-susceptibility were limited by insufficient statistical power. Here, we aim to clarify the putative association between CNTN5 CNVs and ASD-risk using large-scale case-control analyses. MethodA CNTN5 CNV, shared by four brothers in a multiplex family with ASD, was initially identified. We calculated the prevalence and transmission of CNTN5 CNVs in cases across five ASD cohorts (n=15,784). Second, we compared the prevalence of CNTN5 CNVs in cases to their unaffected siblings (n=4,996). Third, we assessed the enrichment of CNTN5 CNVs in cases to extrafamilial controls across three cohorts (n=24,886) and the UK Biobank (n = 459,862). Finally, we evaluated the clinical impact of CNTN5 CNVs in a broad neurodevelopmental disorder cohort and the DECIPHER database. ResultsMost (96.7%) CNTN5 CNV deletions (0.193%) and duplications (0.03%) in cases were inherited by a parent that transmitted the variant to their affected and unaffected children at the same rate. We identified a significant enrichment of intronic CNTN5 CNV deletions in cases compared to extrafamilial controls (0.178% versus 0.019%; p-value=1.68E-05; OR:8.51; 95%CI=[2.58-44.21]). There was no difference in CNTN5 CNV enrichment between cases and individuals with NDDs. ConclusionsIntronic CNTN5 CNV deletions are rare, inherited, and intermediate effect size ASD-susceptibility variants that may also confer risk for other neuropsychiatric disorders. We offer a framework to characterize candidate variants that may not be detected through small-scale approaches to implicate intermediate effect size variants in the etiology of ASD.

Splicing variants in NARS2 are associated with milder phenotypes and intra-familial variability

Biallelic rare variants in NARS2 that encode the mitochondrial asparaginyl-tRNA synthetase are associated with a wide spectrum of clinical phenotypes ranging from severe neurodegenerative disorders to isolated mitochondrial myopathy or deafness. To date, only a small number of patients with NARS2 variants have been reported, and possible genotype-phenotype correlations are still lacking. Here, we present three siblings who had an early-onset hearing loss, while one developed severe symptoms in adulthood associated with early intellectual impairment, refractory seizures, moderate axonal sensorimotor neuropathy, and atypical psychiatric symptoms. Biochemical analysis revealed impairment of the activity and assembly of the respiratory chain complexes in this patient's muscle and fibroblasts. Whole Exome Sequencing allowed identification of a heterozygous variant NM_024678.5(NARS2):c.822G > C (p.Gln274His) that is known to be pathogenic and to affect splicing of the NARS2 gene, but was unable to detect a second variant in this gene. Coverage analysis and Sanger sequencing led to identification of a novel intronic deletion NM_024678.5(NARS2):c.922-21_922-19del in the three siblings in trans with the c.822G > C. Functional analysis by RT-PCR showed that this deletion was causing aberrant splicing and led to exon 9 skipping in NARS2 mRNA in patient fibroblasts. Our work expands the phenotype and genotype spectrum of NARS2-related disorders. We provide evidence of the pathogenic effect of a novel intronic deletion in the NARS2 gene and report on additional adult patients with a large intrafamilial variability associated with splice variants in this gene. More specifically, we detail the phenotype of the oldest living patient to date with NARS2 variants and, for the first time, we report the psychiatric symptoms associated with this gene. Our work confirms the complexity of genotype-phenotype correlation in patients with pathogenic NARS2 variants.

A GE:-13 (GECT-) HETEROZIGOUS AND GE:-14 (GEAR) HOMOZIGOUS PHENOTYPE DETECTED BY RANDOM SCREENING FOR GE:-2 BLOOD DONORS IN BRAZIL

We report a rare case of GE:-13 and GE:-14 phenotype blood donor identified by random screening during blood bank routine. This is a descriptive work using immunohematology data from immunohematology reference laboratory (LRI) where samples were tested. A 29 year old blood donor, woman, self-declared as african american from the São Paulo city with no history of previous transfusions or pregnancies. Her blood was typed as O RhD+ (C-E+c+e+) and K- and the antibody screening was negative in gel cards. The phenotypes identified as Ge:-2,3 were confirmed by screening for GE:-2 blood group performed by hemagglutination in DG Gel cards using in house anti-Ge2 and others anti-Ge2 and anti-Ge3 from our inventory. Genomic DNA was isolated from donor whole blood and GE genotyping was performed by PCR-SSP techniques for analysis of exons 2, 3 and exon 4. The genetic variations that influence the expression of high-incidence antigens are deletions that involve exons 2, 3, 4 and the single nucleotide exchange (SNVs) in exons regions of the GYPC gene. These mutations, if not studied by molecular tests, may result in serological interpretation errors. Thus, sequencing by Sanger method of GE gene was performed and revealed a nucleotídeo change 59C>T (Pro20Leu in GPC) in Exon 2 in heterozygous and a nucleotide change 333A>C (non-coding) (Gly19Arg in GPD) in Exon 4 in homozigous state. No other nucleotide changes were identified. One of the criteria for AABB reference laboratory certification in immunohematology is the screening for blood donors with rare phenotypes. For this reason, donors from the Hospital Israelita Albert Einstein are tested with anti-Ge2 antiserum. The aim is detect the rare phenotype Ge:-2, for compatibility tests in patients with anti-Ge2 alloantibody. The antigens of the Gerbich System are located on glycophorins C (GPC), D (GPD) or both. There are eight highly prevalent antigens known as Ge2, Ge3, Ge4, GEPL, GEAT, GETI, GECT, GEAR. Polymorphisms that involve high incidence antigens such as deletions in introns and single nucleotide exchange (SNVs) in exons regions of the GYPC gene, if not studied by molecular tests, may result in serological interpretation errors. The fact of donor has a GECT allele (GE*01.-13) in heterozygosity does not imply the development of antibodies. The homozygous GEAR allele (GE*01-14) could result in the production of a rare anti-GEAR antibody in case of transfusion or pregnancy, however the clinical importance of this antibody is still unknown. Few articles report that these mutations can lead to loss of epitopes and the phenotypes can be interpreted as Ge:-2 or Ge:-3 in serological screening. This case showed that the molecular sequencing was crucial to determine the correct mutations present in the GYPC gene and consequently the correct deduction of the phenotype.

Megaconial congenital muscular dystrophy due to novel CHKB variants: a case report and literature review

BackgroundCholine kinase beta (CHKB) catalyzes the first step in the de novo biosynthesis of phosphatidyl choline and phosphatidylethanolamine via the Kennedy pathway. Derangement of this pathway might also influence the homeostasis of mitochondrial membranes.Autosomal recessive CHKB mutations cause a rare form of congenital muscular dystrophy known as megaconial congenital muscular dystrophy (MCMD).Case presentationWe describe a novel proband presenting MCMD due to unpublished CHKB mutations. The patient is a 6-year-old boy who came to our attention for cognitive impairment and slowly progressive muscular weakness. He was the first son of non-consanguineous healthy parents from Sri Lanka. Neurological examination showed proximal weakness at four limbs, weak osteotendinous reflexes, Gowers’ maneuver, and waddling gate. Creatine kinase levels were mildly increased. EMG and brain MRI were normal. Left quadriceps skeletal muscle biopsy showed a myopathic pattern with nuclear centralizations and connective tissue increase. Histological and histochemical staining suggested subsarcolemmal localization and dimensional increase of mitochondria. Ultrastructural analysis confirmed the presence of enlarged (“megaconial”) mitochondria. Direct sequencing of CHKB identified two novel defects: the c.1060G > C (p.Gly354Arg) substitution and the c.448-56_29del intronic deletion, segregating from father and mother, respectively. Subcloning of RT-PCR amplicons from patient’s muscle RNA showed that c.448-56_29del results in the partial retention (14 nucleotides) of intron 3, altering physiological splicing and transcript stability. Biochemical studies showed reduced levels of the mitochondrial fission factor DRP1 and the severe impairment of mitochondrial respiratory chain activity in patient’s muscle compared to controls.ConclusionsThis report expands the molecular findings associated with MCMD and confirms the importance of considering CHKB variants in the differential diagnosis of patients presenting with muscular dystrophy and mental retardation. The clinical outcome of MCMD patients seems to be influenced by CHKB molecular defects. Histological and ultrastructural examination of muscle biopsy directed molecular studies and allowed the identification and characterization of an intronic mutation, usually escaping standard molecular testing.

Intraspecific comparison of mitochondrial genomes reveals the evolution in medicinal fungus Ganoderma lingzhi

Several mitogenomes of the genus Ganoderma have been assembled, but intraspecific comparisons of mitogenomes in Ganoderma lingzhi have not been reported. In this study, 19 G.lingzhi mitogenomes were assembled and analyzed combined with three mitogenomes of G.lingzhi from GenBank in term of the characteristics, evolution, and phylogeny. The results showed that the mitogenomes of the G.lingzhi strains are closed circular ranging from 49.23kb to 68.37kb. The genetic distance, selective pressure, and base variation indicate that the 14 common protein coding genes were highly conserved. The differences in introns, open reading frames, and repetitive sequences in the mitogenome were the main factors leaded to the variations in mitogenome. The introns were horizontally transferred in mitogenomes, and the differences between introns in the same insertion, which were primarily caused by the repetitive sequence, showed that the introns may be under degeneration. Besides, the frequent insertion and deletion of introns showed an evolutionary rate faster than protein coding genes. Phylogenetic analysis showed that the G.lingzhi strains gathered with high support, and those with the same intron distribution law had closer clustering relationships.

Introns in the Naa50 gene act as strong enhancers of tissue-specific expression in Arabidopsis

Naa50 is the catalytic subunit of N-terminal acetyltransferase complex E, which plays an important role in regulating plant development, endoplasmic reticulum stress and immune responses in Arabidopsis. In this study, the complete genomic sequence (but not the coding sequence) of Naa50 rescued the phenotype of Naa50 deletion mutants. Naa50 expression was noted in whole roots except for central root cap cells. The deletion of intron 1 resulted in a loss of Naa50 expression in the root meristem zone and in the epidermis, cortex and endodermis of the elongation zone and mature zone, while the deletion of intron 2 decreased Naa50 expression in the epidermis, cortex and endodermis of the root elongation zone and mature zone. The native Naa50 promoter together with introns 1 and 2 promotes the expression of Naa50 in sepal vascular bundles, filaments, pollen and stigmas; however, neither intron has positive effect on Naa50 expression in mature rosette leaves. The results of this study show that introns 1 and 2 in the Naa50 gene function as enhancers to promote the tissue-specific expression of Naa50.

Identification of the first congenital ichthyosis case caused by a homozygous deletion in the ALOX12B gene due to chromosome 17 mixed uniparental disomy.

Uniparental disomy (UPD) is a rare genetic event caused by errors during gametogenesis and fertilization leading to two copies of a chromosome or chromosomal region inherited from one parent. MixUPD is one type of UPD that contains isodisomic and heterodisomic parts because of meiotic recombination. Using whole-exome sequencing (WES), we identified the first case of ichthyosis due to a maternal mixUPD on chromosome 17, which results in a homozygous deletion of partial intron 8 to exon 10 in ALOX12B, being predicted to lead to an internal protein deletion of 97 amino acids. We also performed a retrospective analysis of 198 patients with ALOX12B mutations. The results suggested that the exon 9 and 10 are located in the mutational hotspots of ALOX12B. In addition, our patient has microtia and congenital stenosis of the external auditory canals, which is very rare in patients with ALOX12B mutations. Our study reports the first case of autosomal recessive congenital ichthyosis (ARCI) due to a mixUPD of chromosome 17 and expands the spectrum of clinical manifestations of ARCI caused by mutations in the ALOX12B gene.

Biallelic and gene-wide genomic substitution for endogenous intron and retroelement mutagenesis in human cells

Functional annotation of the vast noncoding landscape of the diploid human genome still remains a major challenge of genomic research. An efficient, scarless, biallelic, and gene-wide mutagenesis approach is needed for direct investigation of the functional significance of endogenous long introns in gene regulation. Here we establish a genome substitution platform, the Universal Knock-in System or UKiS, that meets these requirements. For proof of concept, we first used UKiS on the longest intron of TP53 in the pseudo-diploid cell line HCT116. Complete deletion of the intron, its substitution with mouse and zebrafish syntenic introns, and specific removal of retrotransposon-derived elements (retroelements) were all efficiently and accurately achieved in both alleles, revealing a suppressive role of intronic Alu elements in TP53 expression. We also used UKiS for TP53 intron deletion in human induced pluripotent stem cells without losing their stemness. Furthermore, UKiS enabled biallelic removal of all introns from three human gene loci of ~100 kb and longer to demonstrate that intron requirements for transcriptional activities vary among genes. UKiS is a standard platform with which to pursue the design of noncoding regions for genome writing in human cells.

Association analysis of indels in the VISFATIN gene with five cattle breeds and their growth traits

VISFATIN is an adipose cytokine that has been proved to correlate with growth and development traits. In a previous study from our lab, two insertion/deletions (indels; including a 35-bp insertion at its intron 4 and a 6-bp deletion in intron 5) were identified within the VISFATIN gene. To validate these indels and evaluate their association with growth traits in Chinese cattle, a total of 413 samples from four Chinese indigenous breeds and 217 samples from Chinese breeds were detected. Three genotypes (WW, WI and II) at intron 4 were detected based on the 35-bp insertion (allele I) or deletion (allele W) and showed moderate polymorphism in all samples. Two genotypes (WW and WD) at intron 5 were detected based on the 6-bp deletion (allele D) or insertion (allele W) in Xianan (XN) cattle and Jinnan (JN) cattle population but showed poor polymorphisms. Association analysis illustrated that the indel at intron 4 is significantly associated with chest girth, rump length and body weight in Ji'an (JA) cattle and the indel at intron 5 can cause a significant difference in rump length in JN cattle. To our knowledge, it is the first time it has been shown that indels within the VISFATIN gene are associated with growth traits in the two Chinese indigenous cattle breeds. These findings suggest that the VISFATIN gene can be used as a molecular marker for JN and JA cattle breeding.

PB1792: NGS VS PCR FOR THE DETECTION OF NPM1 GENE MUTATIONS IN ACUTE MYELOID LEUKEMIA.

Background:NPM1 gene mutations are found in 30% of acute myeloid leukemia (AML) cases. It is a reliable marker for the evaluation of therapy outcome and minimal residual disease (MRD) monitoring. The most often mutations are 4bp insertions in exon 12, affecting 2 functionally important tryptophan residues (W288 and W290) in the C-terminal region of nucleophosmin and causing a frameshift. As a result, a leucine-rich motif (L-xxx-V-xx-V-x-L) is formed, which is a signal sequence for protein export from the nucleus to the cytoplasm. Commonly NPM1 gene mutations are detected by fragment analysis (FA) of PCR fragment of 12 exon for the presence of 4bp insert. Alternatively, allele-specific polymerase chain reaction (AS-PCR) to detect inserts belonging to the A, B, or D type (representing up to 90% of all inserts) is used. However, about 10% remaining cases are non-standard inserts and intron polymorphisms that require more precise evaluation. Aims: Evaluation of diverse approaches for efficient NPM1 gene mutation analysis and their robustness for the diagnostics. Methods: The study included 80 DNA samples from AML patients admitted to the National Research Center for Hematology in 2019-2021 that were positive for NPM1 gene mutations detected by FA performed with the Nanophor-5 genetic analyzer (Synthol, Russia). The type of insert was assessed by AC-PCR. Samples in doubt were evaluated by targeted next-generation sequencing (NGS) on MySeq (Illumina, USA). Results: In 62 out of 80 samples, the type of insert (A, B, or D) was reliably determined by AS-PCR. In 9 cases type of insert was not detected. In further 9 cases, amplification ΔCt between wild-type and mutant allele was out of reliable range. These 18 samples were examined by NGS, and 2 out of 18 showed an intron deletion, which, presumably, does not affect the function of the protein, but leads to the appearance of an additional peak on FA. In 16 out of 18 samples, non-standard inserts were detected (Table 1). Type A inserts were found in 48 out of 78 cases (61.5%), type B - in 2 out of 78 (4.5%), and type D - 15.4% (12 out of 78). We have detected atypical inserts in 16 out of 78 cases (20.5%), which is more than reported in the literature. 14 out of 16 atypical inserts result in a leucine-rich motif, as do standard inserts. In 4 out of 16 cases, one of the 2 functionally important tryptophan residues was retained (W280), therefore possibly conserving nuclear localization signal. The effect of partial preservation of the nucleolar localization of nucleophosmin on prognosis in AML has not been studied yet. Image:Summary/Conclusion: FA is still a golden standard for screening NPM1 gene mutations in AML. AS-PCR could be effectively used for monitoring cases with standard inserts. However, NGS greatly facilitates non-standard inserts identification, appropriate allele-specific primers design for MRD analysis, and avoiding false-positive FA results for cases with intron localization of the insert.

PTBP2 – a gene with relevance for both Anorexia nervosa and body weight regulation

Genetic factors are relevant for both eating disorders and body weight regulation. A recent genome-wide association study (GWAS) for anorexia nervosa (AN) detected eight genome-wide significant chromosomal loci. One of these loci, rs10747478, was also genome-wide and significantly associated with body mass index (BMI). The nearest coding gene is the Polypyrimidine Tract Binding Protein 2 gene (PTBP2). To detect mutations in PTBP2, Sanger sequencing of the coding region was performed in 192 female patients with AN (acute or recovered) and 191 children or adolescents with (extreme) obesity. Twenty-five variants were identified. Twenty-three of these were predicted to be pathogenic or functionally relevant in at least one in silico tool. Two novel synonymous variants (p.Ala77Ala and p.Asp195Asp), one intronic SNP (rs188987764), and the intronic deletion (rs561340981) located in the highly conserved region of PTBP2 may have functional consequences. Ten of 20 genes interacting with PTBP2 were studied for their impact on body weight regulation based on either previous functional studies or GWAS hits for body weight or BMI. In a GWAS for BMI (Pulit et al. 2018), the number of genome-wide significant associations at the PTBP2 locus was different between males (60 variants) and females (two variants, one of these also significant in males). More than 65% of these 61 variants showed differences in the effect size pertaining to BMI between sexes (absolute value of Z-score >2, two-sided p < 0.05). One LD block overlapping 5′UTR and all coding regions of PTBP2 comprises 56 significant variants in males. The analysis based on sex-stratified BMI GWAS summary statistics implies that PTBP2 may have a more pronounced effect on body weight regulation in males than in females.

Analysis of MET genetic aberrations in Chinese solid tumor patients.

e15031 Background: Mesenchymal-epithelial transition (MET) gene encodes a member of the receptor tyrosine kinase family of proteins and is a proto-oncogene. MET gene takes part in various signaling pathways such as PI3K/AKT, Ras/MAPK, and JAK/STAT which are associated with tumor development and progression. This study aimed to reveal MET aberrated characteristics in Chinese solid tumor patients and explore the occurrence of MET oncogenic variants in solid tumors. Methods: This study retrospectively analyzed MET alterations in 1856 solid tumor patients in China from laboratory of Simcere Diagnosis (Nanjing, China) during 2019-2021. Next-generation sequencing (NGS) was performed to detect gene mutations in tumor or blood samples of the patients. Results: We screened out 1856 patients with MET gene alterations from 45717 patients with solid tumor. The high frequency of MET gene alterations was lung cancer (72.8%), colorectal cancer (10.7%), gastric cancer (4.9%), and liver cancer (2.7%). MET gene variants included missense (61.7%), copy number variation (copy number≥5) (15.4%), truncation (7.9%), splicing site variant (7.2%),fusion (1.7%),and in-frame insertion/deletions (0.9%). Among them, MET amplification was detected in 285 patients, and 93 patients carried high-level MET amplification (copy number≥10). High-level MET amplification was most frequently detected in lung cancer (41, 44.1%), gastric cancer (17, 18.3%) and liver cancer (14, 15.1%). MET exon 14 skipping was detected in 287 solid tumor patients (15.5%), of which 277 patients were lung cancer, the remaining were liver cancer, colorectal cancer, gastric cancer, osteosarcoma, melanoma, bladder cancer and glioma. We analyzed MET exon 14 alterations and classified them into 4 subgroups according to the alteration types and locations. The most common alterations were at splice donor sites (215, 74.91%), followed by the splice acceptor sites (35, 12.20%), Y1003 site (5, 1.74%), and other types (32, 11.15%). Other types included insertion or deletion in MET intron 13 or 14, for example, c.3028+21_3028+65del, c.2888-20_2888-11del, c.2888-27_2888-9del, etc. 7 lung cancer patients carried MET exon 14 skipping and MET amplification simultaneously. 36 patients carried MET gene fusions, and mostly were lung cancer (22, 61.1%). The breakpoints often located in exon 2 of MET (4, 11.1%). Conclusions: We discovered MET alterations in multiple types of solid tumors in this study. We found classic MET exon 14 skipping and MET high-level amplification in solid tumors except for lung cancer. It suggested that the activation of MET-driven signaling pathway was ubiquitous in pan-cancer, which might benefit from MET inhibitors.

Identification and Characterization of Variants in Intron 6 of the LPL Gene Locus among a Sample of the Kuwaiti Population.

Lipoprotein lipase (LPL) is responsible for the hydrolysis of lipoproteins; hence defective LPL is associated with metabolic disorders. Here, we identify certain intronic insertions and deletions (InDels) and single nucleotide polymorphisms (SNPs) in intron 6 of the LPL gene and investigate their associations with different phenotypic characteristics in a cohort of the general Kuwaiti population. Two specific regions of intron 6 of the LPL gene, which contain InDels, were amplified via Sanger sequencing in 729 subjects. Genotypic and allelic frequencies were estimated, and genetic modeling was used to investigate genetic associations of the identified variants with lipid profile, body mass index (BMI), and risk of coronary heart disease (CHD). A total of 16 variants were identified, including 2 InDels, 2 novel SNPs, and 12 known SNPs. The most common variants observed among the population were rs293, rs274, rs295, and rs294. The rs293 “A” insertion showed a significant positive correlation with elevated LDL levels, while rs295 was significantly associated with increased BMI. The rs274 and rs294 variants showed a protective effect of the minor allele with decreased CHD prevalence. These findings shed light on the possible role of LPL intronic variants on metabolic disorders.

Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy.

DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reactionor high-throughput RNA sequencingmethods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.

C1: Targeting mutational landscape of TP53 gene in patients diagnosed with oral cancers living in Senegal

INTRODUCTION: Looking for the mutational landscape on a genomic scale has provided in the last few years unprecedented perspectives for understanding molecular pathogenesis of cancer progression, response to treatment and genetic predisposition. In oral cancers, numerous genomic studies have been devoted to alterations in the TP53 gene and their clinical significance in carcinogenesis. Herein, we screened for genomic variants of TP53 predisposing to oral cancers in Senegalese patients. MATERIALS AND METHODS: Eighty-eight patients with confirmed diagnostic were recruited after informed consent from Stomatology Unit of Aristide le Dantec Hospital. Blood samples were collected from each patient to perform DNA extraction, PCR amplification of all coding exons of TP53 followed by Sanger Sequencing of PCR products. Nucleotidic sequences were analyzed with Genalys software. RESULTS: Mean age at diagnosis was estimated at 51.9 ± 17.98 years with a sex-ratio of 0.76. The majority of patients (64/88) had a negative alcohol-tobacco status. Tumor histology showed that 90% of patients had squamous cell carcinoma localised preferentially on the tongue (22.7%), gum (20.5%) and cheek mucosa (19.3%). Mutation screening of TP53 showed that 52.27% of the patients carried at least one mutation. Eleven genomic variants were identified, seven already reported in mutation databases and four new variants. The most recurrent variants was p.Pro72Arg (rs1042522; Arginine allelic frequency estimated at 31.26%) and a 16 bp deletion in intron 3 (rs59758982; allelic frequency estimated at 26.25%). Linkage disequilibrium (LD) calculation has shown that these two variants are in strong LD but tests of association with controls show that they could not predispose towards oral cancers. CONCLUSION: The results of the present investigation suggest that the two most common variants found in Senegalese patients are not predisposing to oral cancers. Further comprehensive investigations on reported and new variants found in this study should be conducted to highlight their functional impacts and hypothetic oncogenic associated function.

Molecular Dissection of Structural Variations Involved in Antithrombin Deficiency

Inherited antithrombin deficiency, the most severe form of thrombophilia, is predominantly caused by variants in SERPINC1. Few causal structural variants have been described, usually detected by multiplex ligation-dependent probe amplification or cytogenetic arrays, which only define the gain or loss and the approximate size and location. This study has done a complete dissection of the structural variants affecting SERPINC1 of 39 unrelated patients with antithrombin deficiency using multiplex ligation-dependent probe amplification, comparative genome hybridization array, long-range PCR, and whole genome nanopore sequencing. Structural variants, in all cases only affecting one allele, were deleterious and caused a severe type I deficiency. Most defects were deletions affecting exons of SERPINC1 (82.1%), but the whole cohort was heterogeneous, as tandem duplications, deletion of introns, or retrotransposon insertions were also detected. Their size was also variable, ranging from 193 bp to 8 Mb, and in 54% of the cases involved neighboring genes. All but two structural variants had repetitive elements and/or microhomologies in their breakpoints, suggesting a common mechanism of formation. This study also suggested regions recurrently involved in structural variants causing antithrombin deficiency and found three structural variants with a founder effect: the insertion of a retrotransposon, duplication of exon 6, and a 20-gene deletion. Finally, nanopore sequencing was determined to be the most appropriate method to identify and characterize all structural variants at nucleotide level, independently of their size or type.

The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships.

The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.