Relevant Copy Number Research Articles

Array Comparative Genomic Hybridization (aCGH) Results among Patients Referred to Invasive Prenatal Testing after First-Trimester Screening: A Comprehensive Cohort Study.

Introduction: Invasive prenatal testing with chromosomal microarray analysis after first-trimester screening is a relevant option but there is still debate regarding the indications. Therefore, we evaluated the prevalence of numerical chromosomal aberrations detected by classic karyotype and clinically relevant copy number variants (CNVs) in prenatal samples using array comparative genomic hybridization (aCGH) stratified to NT thickness: <the 95th percentile, the 95th percentile-2.9 mm, 3.0-3.4 mm, 3.5-3.9 mm, 4.0-4.5 mm, and >4.5 mm, and by the presence/absence of associated structural anomalies detected by ultrasonography. Materials and Methods: Retrospective cohort study carried out at two tertiary Polish centers for prenatal diagnosis (national healthcare system) in central and south regions from January 2018 to December 2021. A total of 1746 prenatal samples were received. Indications for invasive prenatal testing included high risk of Down syndrome in the first-trimester combined test (n = 1484) and advanced maternal age (n = 69), and, in 193 cases, other reasons, such as parental request, family history of congenital defects, and genetic mutation carrier, were given. DNA was extracted directly from amniotic fluid (n = 1582) cells and chorionic villus samples (n = 164), and examined with classic karyotype and aCGH. Results: Of the entire cohort of 1746 fetuses, classical karyotype revealed numerical chromosomal aberrations in 334 fetuses (19.1%), and aCGH detected CNV in 5% (n = 87). The frequency of numerical chromosomal aberrations increased with NT thickness from 5.9% for fetuses with NT < p95th to 43.3% for those with NT > 4.5 mm. The highest rate of numerical aberrations was observed in fetuses with NT > 4.5 mm having at least one structural anomaly (50.2%). CNVs stratified by NT thickness were detected in 2.9%, 2.9%, 3.5%, 4.3%, 12.2%, and 9.0% of fetuses with NT < 95th percentile, 95th percentile-2.9 mm, 3.0-3.4 mm, 3.5-3.9 mm, 4.0-4.5 mm, and >4.5 mm, respectively. After exclusion of fetuses with structural anomalies and numerical aberrations, aCGH revealed CNVs in 2.0% of fetuses with NT < 95th percentile, 1.5% with NTp95-2.9 mm, 1.3% with NT 3.0-3.4 mm, 5.4% with NT 3.5-3.9 mm, 19.0% with NT 4.0-4.5 mm, and 14.8% with NT > 4.5 mm. Conclusions: In conclusion, our study indicates that performing aCGH in samples referred to invasive prenatal testing after first-trimester screening provides additional clinically valuable information over conventional karyotyping, even in cases with normal NT and anatomy.

Contribution of clinically relevant copy number variations in long QT syndrome: a large cohort study

Abstract Background Copy number variations (CNVs) have increasingly been recognized in the cardiovascular setting. Their role in hypertrophic cardiomyopathy or sudden cardiac death has been described, but their involvement in Long QT syndrome (LQTS) has been scarcely studied. Most of these descriptions are confined to case reports or small series. Purpose The aim of this study is to investigate the proportion of clinically relevant CNVs among a large cohort of index cases referred for genetic testing due to LQTS. Methods Retrospective study in which the presence of likely pathogenic (LP) or pathogenic (P) CNVs was evaluated in a cohort of index cases referred for genetic study with LQTS phenotype. Index cases were genotyped with customized libraries through next generation sequencing (NGS). CNVs analysis was conducted by a proprietary method by means of comparative analysis of normalized read depth data. Clinically relevant (LP or P) CNVs were then confirmed by other techniques. Results 1183 index cases were referred for genetic testing to our laboratory with long QT syndrome phenotype. Some of these index cases were referred for suspicion of Jervell-Lange-Nielsen syndrome (JNLS) or for LQTS associated with congenital deafness (n=10) or Anderson-Tawil syndrome (n=1). Around 27% (n=322) of the index cases had a positive result. CNVs analysis was run on 1071 (91%) of the index cases. Most of the CNVs were considered negative (n=994, 93%), 59 could not be analysed (6%) and in 11 patients (1%), a LP/P CNV was identified. All CNVs but three (72.72%), were confirmed by orthogonal molecular techniques (Sanger sequencing or multiplex ligation-dependent probe amplification (MLPA)). In all, but two, the genetic study was considered positive due to the CNV findings. One of these patients carried a pathogenic lost-of-function (LOF) CNV in the LDLR gene (incidental finding) but the report was negative because he was referred for suspicion of JLNS. In another case a CNV in the DSP gene was identified in mosaicism (30-40%). However, in this case, the positive report was attributed to the presence of an additional pathogenic variant in CACNA1C. Regarding the other index cases with LP/P CNVs: 4 carried a deletion in the KCNH2 gene, 3 carried a deletion in KCNQ1 gene (one of them in homozygosis and was studied for suspicion of JLNS) and 1 carried a duplication in the KCQN1 (LOF variant). In addition, one patient carried a deletion of exon 3 in the RYR2 gene. Even if the patient was referred for suspicion of LQTS, the report was considered positive. These clinically relevant CNVs represented around 3% of the positive genetic results. Conclusions In our large cohort of patients referred for genetic testing for LQTS, around 1% of clinically relevant CNVs were identified. As such large genomic rearrangements underlie a non-neglectable portion of cases, we consider that their analysis should be performed as part of the routine genetic testing.Deletion exons 6-14 in KCNH2 gene (CNV)MLPA with deletion exons 6-14 in KCNH2

Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors.

Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.

Streamlined identification of clinically and functionally relevant genetic regulators of lower-tract urogenital development

Congenital anomalies of the lower genitourinary (LGU) tract are frequently comorbid due to genetically linked developmental pathways, and are among the most common yet most socially stigmatized congenital phenotypes. Genes involved in sexual differentiation are prime candidates for developmental anomalies of multiple LGU organs, but insufficient prospective screening tools have prevented the rapid identification of causative genes. Androgen signaling is among the most influential modulators of LGU development. The present study uses SpDamID technology in vivo to generate a comprehensive map of the pathways actively regulated by the androgen receptor (AR) in the genitalia in the presence of the p300 coactivator, identifying wingless/integrated (WNT) signaling as a highly enriched AR-regulated pathway in the genitalia. Transcription factor (TF) hits were then assayed for sexually dimorphic expression at two critical time points and also cross-referenced to a database of clinically relevant copy number variations to identify 252 TFs exhibiting copy variation in patients with LGU phenotypes. A subset of 54 TFs was identified for which LGU phenotypes are statistically overrepresented as a proportion of total observed phenotypes. The 252 TF hitlist was then subjected to a functional screen to identify hits whose silencing affects genital mesenchymal growth rates. Overlap of these datasets results in a refined list of 133 TFs of both functional and clinical relevance to LGU development, 31 of which are top priority candidates, including the well-documented renal progenitor regulator, Sall1. Loss of Sall1 was examined in vivo and confirmed to be a powerful regulator of LGU development.

Diagnostic yield and novel candidate genes for neurodevelopmental disorders by exome sequencing in an unselected cohort with microcephaly

ObjectivesMicrocephaly is caused by reduced brain volume and most usually associated with a variety of neurodevelopmental disorders (NDDs). To provide an overview of the diagnostic yield of whole exome sequencing (WES) and promote novel candidates in genetically unsolved families, we studied the clinical and genetic landscape of an unselected Chinese cohort of patients with microcephaly.MethodsWe performed WES in an unselected cohort of 103 NDDs patients with microcephaly as one of the features. Full evaluation of potential novel candidate genes was applied in genetically undiagnosed families. Functional validations of selected variants were conducted in cultured cells. To augment the discovery of novel candidates, we queried our genomic sequencing data repository for additional likely disease-causing variants in the identified candidate genes.ResultsIn 65 families (63.1%), causative sequence variants (SVs) and clinically relevant copy number variants (CNVs) with a pathogenic or likely pathogenic (P/LP) level were identified. By incorporating coverage analysis to WES, a pathogenic or likely pathogenic CNV was detected in 15 families (16/103, 15.5%). In another eight families (8/103, 7.8%), we identified variants in newly reported gene (CCND2) and potential novel neurodevelopmental disorders /microcephaly candidate genes, which involved in cell cycle and division (PWP2, CCND2), CDC42/RAC signaling related actin cytoskeletal organization (DOCK9, RHOF), neurogenesis (ELAVL3, PPP1R9B, KCNH3) and transcription regulation (IRF2BP1). By looking into our data repository of 5066 families with NDDs, we identified additional two cases with variants in DOCK9 and PPP1R9B, respectively.ConclusionOur results expand the morbid genome of monogenic neurodevelopmental disorders and support the adoption of WES as a first-tier test for individuals with microcephaly.

Abstract 6220: Development of a mutation profiling NGS assay to facilitate clinical decisions in hematologic malignancies

Abstract Introduction: Accurate diagnosis, prognosis and treatment of hematologic disorders from both myeloid and lymphoid origin requires assessing somatic mutation status in an increasingly large number of genes. Here we present the results of the assay development and validation of a targeted next generation sequencing panel which provides full exon sequencing of 141 genes associated with myeloid and lymphoid malignancies, as well as the ability to detect clinically relevant copy number alterations (CNAs) and certain sub-gene level CNAs. Methods: Based on review of clinical guidelines, 141 genes including 72 myeloid and 84 lymphoid associated genes were selected. The assay interrogates all coding exons of the 141 genes to detect single nucleotide variants (SNVs) and insertions/deletions (indels). The assay also identifies CNAs in 16 genes, FLT3 internal tandem duplicates (ITDs), and select non-coding pathogenic variants. The custom hybrid capture-based assay utilizes genomic libraries created from 250 ng gDNA extracted from peripheral blood or bone marrow followed by sequencing on Illumina sequencers. Concordance studies were performed on clinical samples previously assessed using an orthogonal NGS-based laboratory developed test for SNVs/Indels or digital multiplexed ligation-dependent probe amplification for CNAs. In addition, analytical sensitivity was assessed using cell line dilution series and specificity by reference samples from Genome in a Bottle (GIAB). Small indels were defined as &amp;lt;25bp while long indels are ≥ 25bp. Results: Interim estimates of positive percentage agreement (PPA) and specificity have been determined for SNV/Indels, FLT3-ITDs, and CNVs, with further testing ongoing. PPA of SNVs was 100% (218/218 SNVs; n = 134 samples). PPA was also 100% for both small indels (21/21; n = 14 samples) and long indels (6/6; n = 6 samples). A dilution series of 8 positive clinical samples at 4 different dilutions showed SNV and small indel detection of 100% at allele frequency (AF) ≥ 3%. Long indel detection was 87.5% at AF ≥ 5%. FLT3-ITD was evaluated with 2 cell line samples at 5 different dilutions with 100% detection at AF ≥ 5%. PPA of CNAs were 95.7% (157/164) in 46 clinical samples. CNA detection was also evaluated with 8 cell line samples at 4 different dilutions showing 92.3% detection at a copy number ratio threshold ± 0.15. A preliminary estimate of specificity was determined using 4 replicates of the GIAB sample, NA12878, and was &amp;gt;99.99% for SNVs and small indels (n=6.9 × 105). Finally, a model for gender classification was created using a training cohort of 70 clinical samples. The performance was evaluated on a test set of 144 clinical samples with 100% PPA (144/144). Conclusions: Taken together, these data demonstrate that the developed NGS assay is a sensitive, specific, and accurate assay with high clinical utility to inform treatment decision making in hematologic malignancies. Citation Format: Grant Hogg, Tong Liu, Helen Cao, Adib Shafi, Ashraf Shabaneh, John Howitt, Amanda Williamson, Rachel Dango, Xiaojun Guan, Heidi Hoffmann, Michael Mooney, John Pruitt, Scott Parker, Stan Letovsky, Li Cai, Eric A. Severson, Shakti Ramkissoon, Anjen Chenn, Marcia Eisenberg, Eyad Almasri, Taylor Jensen. Development of a mutation profiling NGS assay to facilitate clinical decisions in hematologic malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6220.

Should Prenatal Chromosomal Microarray Analysis Be Offered for Pulmonary Atresia? A Single-Center Retrospective Study in China.

(1) Objective: To evaluate the application of chromosomal microarray analysis (CMA) in fetuses with pulmonary atresia (PA) and to explore the risk factors for predicting chromosomal imbalances and adverse perinatal outcomes. (2) Methods: This study investigated 428 cases of PA singleton pregnancies that were tested using CMA and quantitative fluorescent polymerase chain reaction (QF-PCR) as first-line genetic testing. The PA cases were divided into two groups: an isolated group and a non-isolated group. (3) Results: CMA revealed clinically relevant copy number variations (CNVs) in 9/139 (6.47%) PA fetuses, i.e., pathogenic copy number variations (pCNVs) in 8/139 (5.76%) fetuses and likely pathogenic CNVs in 1/139 (0.72%) fetuses. Stratified analysis showed that the incidence of clinically significant variants was higher in non-isolated PA fetuses than in isolated PA fetuses (12.50%, 6/48 vs. 3.30%, 3/91, p = 0.036). Regression analysis showed that a combination of other structural abnormalities at diagnosis of PA represented the principal risk factor for chromosomal imbalances (OR = 2.672). A combination of other structural abnormalities and a high maternal age increased the risk of adverse pregnancy outcomes in PA cases, including intrauterine fetal death (IUFD), termination of pregnancy (TOP), and preterm delivery. (4) Conclusions: The value of CMA for locating imbalanced genetic variations in fetuses with PA was highlighted by this study, particularly when combined with additional structural abnormalities.

Genetic and epigenetic analysis of hepatocellular adenomas with atypical morphological features.

Hepatocellular adenoma (HCA) is a rare liver tumour, which can have atypical morphological features such as cytological atypia, pseudoglandular architecture, and altered reticulin framework. Little is known about the genetic and epigenetic alterations of such HCAs and whether they show the alterations classically found in hepatocellular carcinoma (HCC) or in HCA without atypical morphology. We analysed five HCAs with atypical morphological features and one HCA with transition to HCC. Every tumour was subtyped by immunohistochemistry, sequenced by a targeted NGS panel, and analysed on a DNA methylation microarray. Subtyping of the five HCAs with atypical features revealed two β-catenin mutated HCA (b-HCA), two β-catenin mutated inflammatory HCA (b-IHCA), and one sonic hedgehog activated HCA (shHCA). None of them showed mutations typically found in HCC, such as, e.g. TERT or TP53 mutations. The epigenomic pattern of HCAs with atypical morphological features clustered with reference data for HCAs without atypical morphological features but not with HCC. Similarly, phyloepigenetic trees using the DNA methylation data reproducibly showed that HCAs with morphological atypia are much more similar to nonmalignant samples than to malignant samples. Finally, atypical HCAs showed no relevant copy number variations (CNV). In our series, mutational, DNA methylation, as well as CNV analyses, supported a relationship of atypical HCAs with nonatypical HCAs rather than with HCC. Therefore, in cases with difficult differential diagnosis between HCC and HCA, it might be advisable to perform targeted sequencing and/or combined methylation/copy number profiling.

A generated induced pluripotent stem cell (iPSC) line (CMGANTi005-A) of a Marfan syndrome patient with an FBN1 c.7754T > C (p.Ile2585Thr) variation

Marfan syndrome (MFS) is a connective tissue disorder with pleiotropic manifestations in the ocular, skeletal and cardiovascular system; and is typically cause by pathogenic variants in the fibrillin-1 (FBN1) gene. We report a generated induced pluripotent cell (iPSC) line of a MFS patient with an FBN1 c.7754T > C (p.Ile2585Thr) variant. The cell line was generated from peripheral blood mononuclear cells (PBMCs) and after reprogramming the line showed a no relevant copy number alterations, expression of pluripotency markers and was able to differentiate into three germ layers while carrying the original genotype.

Copy number variation analysis in 189 Romanian patients with global developmental delay/intellectual disability

BackgroundDevelopmental delay and intellectual disability represent a common pathology in general population, involving about 3% of the pediatric age population, the genetic etiology being often involved. The aim of this study was to determine the clinically relevant copy number variants in patients diagnosed with global developmental delay/intellectual disability in our population, using the chromosomal microarray analysis.MethodsWe analyzed 189 patients diagnosed with global developmental delay/intellectual disability, presented in Clinical Emergency Hospital for Children, Cluj-Napoca. The patients were completely clinically investigated, including dysmorphic and internal malformations evaluation, psychiatric, neuropsychological and metabolic evaluation, standard karyotyping. Genomic analysis was done using chromosomal microarray analysis.ResultsPathogenic findings (including uniparental disomy) and variants of unknown significance were detected in 53 of 189 patients (28.04%). Pathogenic copy number variants and uniparental disomy were observed in 35 of 189 patients (18.51%). Two patients presented uniparental disomy for chromosome 15, one with clinical phenotype of Prader-Willi syndrome and the other with clinical phenotype with Angelman syndrome. Within the category of pathogenic findings, the recurrent copy number variants were seen in 21 of 35 patients (60%).ConclusionsThe increased percentage of pathogenic structural variants observed in patients with global developmental delay/intellectual disability analyzed by chromosomal microarray technique supports its use in patients with a non-specific phenotype such as these neurodevelopmental disorders. The high percentage of recurrent pathogenic variants between these findings is a finding that support their initial evaluation when a genetic testing algorithm could be a useful option.

Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas

Classification of gliomas involves the combination of histological features with molecular biomarkers to establish an integrated histomolecular diagnosis. Here, we report on the application and validation of a set of molecular assays for glioma diagnostics based on digital PCR technology using the QX200™ Droplet Digital™ PCR (ddPCR) system. The investigated ddPCR-based assays enable the detection of diagnostically relevant glioma-associated mutations in the IDH1, IDH2, H3-3A, BRAF, and PRKCA genes, as well as in the TERT promoter. In addition, ddPCR-based assays assessing diagnostically relevant copy number alterations were studied, including 1p/19q codeletion, gain of chromosome 7 and loss of chromosome 10 (+ 7/-10), EGFR amplification, duplication of the BRAF locus, and CDKN2A homozygous deletion. Results obtained by ddPCR were validated by other methods, including immunohistochemistry, Sanger sequencing, pyrosequencing, microsatellite analyses for loss of heterozygosity, as well as real-time PCR- or microarray-based copy number assays. Particular strengths of the ddPCR approach are (1) its high analytical sensitivity allowing for reliable detection of mutations even with low mutant allele frequencies, (2) its quantitative determination of mutant allele frequencies and copy number changes, and (3) its rapid generation of results within a single day. Thus, in line with other recent studies our findings support ddPCR analysis as a valuable approach for molecular glioma diagnostics in a fast, quantitative and highly sensitive manner.

EP443: Fetal fraction amplification within NIPS enables detection of clinically-relevant genome-wide copy-number variants to 1Mb resolution

While clinically relevant copy number variants (CNVs) occur in 6-8% of pregnancies with fetal structural anomalies, they are typically difficult to detect via noninvasive prenatal screening (NIPS) because of the low fetal fraction in cell free DNA (cfDNA) isolated from maternal plasma. By leveraging fetal fraction amplification, a method to preferentially sequence shorter fragments that are enriched for fetal-derived cfDNA, we can detect small CNVs with high sensitivity. Here we describe an analytical validation of an NIPS that can detect clinically relevant CNVs across the genome.

Fetal fraction amplification within NIPS enables detection of clinically relevant genome-wide copy-number-variants to 1Mb resolution

While clinically relevant copy number variants (CNVs) occur in 6-8% of pregnancies with fetal structural anomalies, they are typically difficult to detect via noninvasive prenatal screening (NIPS) because of the low fetal fraction in maternal cell-free DNA (cfDNA). By leveraging fetal fraction amplification, a method to preferentially sequence shorter fragments that are enriched for fetal-derived cfDNA, we can detect small CNVs with high sensitivity. Here we describe an analytical validation of an NIPS that can detect clinically relevant CNVs across the genome.

Significance of Low Maternal Serum Β-hCG Levels in the Assessment of the Risk of Atypical Chromosomal Abnormalities

Introduction: The introduction of prenatal cell-free DNA as a screening test has surpassed traditional combined first-trimester screening (cFTS) in the detection of common trisomies. However, its current limitation in detecting only common trisomies is affecting the diagnostic yield for other clinically significant chromosomal abnormalities. Methods: In efforts to optimize the detection of fetuses with genetic abnormalities, we have analyzed the relationship between the cFTS risk score and biomarkers with atypical chromosomal abnormalities. Furthermore, we have evaluated the impact of prenatal cell-free DNA screening on the detection of chromosomal abnormalities in our population. For these purposes, we performed a retrospective study of 877 singleton pregnancies who underwent chromosomal microarray analysis (CMA) between 2013 and 2020 and for whom cFTS data were available. Results: The results demonstrated that low levels of free beta-human chorionic gonadotropin (β-hCG) (≤0.37 multiples of the median) and increased fetal nuchal translucency (NT) (≥3.5 mm) were statistically associated with the presence of atypical chromosomal abnormalities. In fact, the risk of pathogenic CMA results increased from 6 to 10% when fetal NT was increased and from 6 to 20% when a low serum β-hCG level was detected in the high-risk cFTS group. Moreover, our results showed that altered serum levels of β-hCG can have a substantial impact on the early detection of clinically relevant copy number variants. Discussion/Conclusion: Traditional cFTS can potentially identify a substantial proportion of atypical chromosomal aberrations, and women with increased NT or low maternal serum β-hCG levels are at increased risk of having pathogenic CMA results. Our results may help clinicians and women decide whether invasive testing or prenatal cell-free DNA screening testing is more appropriate for each situation.

Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations.

Cell-free DNA (cfDNA) analysis is a minimally invasive method that can be used to detect genomic abnormalities by directly testing a blood sample. This method is particularly useful for immunosuppressed patients, who are at high risk of complications from tissue biopsy. The cfDNA tumor fraction (TF) varies greatly across cancer type and between patients. Thus, the detection of molecular alterations is highly dependent on the circulating TF. In our study, we aimed to calculate the TF and characterize the copy number aberration (CNA) profile of cfDNA from patients with rare malignancies occurring in immunosuppressed environments or immune-privileged sites. To accomplish this, we recruited 36 patients: 19 patients with non-Hodgkin lymphoma (NHL) who were either human immunodeficiency virus (HIV)-positive or organ transplant recipients, 5 HIV-positive lung cancer patients, and 12 patients with glioma. cfDNA was extracted from the patients’ plasma and sequenced using low-coverage whole genome sequencing (LC-WGS). The cfDNA TF was then calculated using the ichorCNA bioinformatic algorithm, based on the CNA profile. In parallel, we performed whole exome sequencing of patient tumor tissue and cfDNA samples with detectable TFs. We detected a cfDNA TF in 29% of immune-suppressed patients (one patient with lung cancer and six with systemic NHL), with a TF range from 8 to 70%. In these patients, the events detected in the CNA profile of cfDNA are well-known events associated with NHL and lung cancer. Moreover, cfDNA CNA profile correlated with the CNA profile of matched tumor tissue. No tumor-derived cfDNA was detected in the glioma patients. Our study shows that tumor genetic content is detectable in cfDNA from immunosuppressed patients with advanced NHL or lung cancer. LC-WGS is a time- and cost-effective method that can help select an appropriate strategy for performing extensive molecular analysis of cfDNA. This technique also enables characterization of CNAs in cfDNA when sufficient tumor content is available. Hence, this approach can be used to collect useful molecular information that is relevant to patient care.

MYC Translocations Identified By Sequencing Panel in Smoldering Multiple Myeloma Strongly Predict for Rapid Progression to Multiple Myeloma

IntroductionSmoldering Myeloma (SMM) is a heterogeneous asymptomatic stage between Monoclonal Gammopathy of Unknown Significance (MGUS) and Multiple Myeloma (MM). Risk of progression to MM is 10% in the first 5 years following diagnosis and greatly diminishes thereafter (Kyle et al NEJM 2007). Early intervention in SMM patients at high risk of progression extends survival (Mateos et al NEJM 2013). The IMWG 2014 Updated Criteria establish a subset of SMM patients who are at ultra-high risk for progression to MM within 2 years, and therefore merit treatment (Rajkumar et al Lancet Oncol 2014). Analyses of the genetic and molecular landscape of SMM to date report a near identical picture to MM, however most patients in these studies progress rapidly and are therefore not representative of the entire group. We performed a comprehensive analysis of SMM and MGUS patients to determine markers of high risk of progression that could identify patients to benefit from early treatmentMethodsMGUS not progressing after at least 10 years of follow up and SMM in which follow up data were available were extracted from the Plasma Cell Dyscrasia Biobank. A clinically applicable Custom Capture MM-specific sequencing platform was developed for detection of the most frequently mutated pathways in MM based on analysis of CoMMpass dataset. Coding exons of actionable genes, clinically relevant copy number abnormalities, and regions surrounding IgH (0.5Mb), IgK (0.1Mb), IgL (0.1Mb) and MYC loci (1.6Mb) to identify relevant structural variants (SVs) were included, with combined design 2.2Mb. 12 samples were pre-pooled before capture, and 2 captures were sequenced per lane of Illumina HiSeq4000. Paired-end 150bp reads were mapped to hg19 using BWA-MEM. Single nucleotide variants (SNVs) and small INDELs in capture regions were identified using the GenomeGPS analytic pipeline following Broad GATK variant discovery practices. Copy number variants (CNVs) were identified by patternCNV. SVs of translocations, inversions, large INDELs, and segmental duplications were called by the SnowShoes-SV algorithm developed in-house. False positive SVs, polymorphic SVs, and other artefacts were filtered out using in-house normal SV database.ResultsWe identified and sequenced 128 patients including 32 MGUS patients not progressing after 10 years. Of 96 SMM patients included 36 had not progressed to SMM after minimum follow up of 5 years, while 37 and 23 progressed to MM in less than 2 years and between 2-5 years, respectively. The genetic subtype of each patient was determined and verified by clinical FISH. Proportions in each genetic subgroup in MM and SMM/MGUS were similar, indicating that these are primary genetic lesions occurring early in MM pathogenesis. Median SMM time to progression (TTP) was 46 months. As in other series, HRD with IGH translocation, and t(4;14) predicted shorter TTP.Analysis of CoMMpass dataset found frequent MYC SV (38%) in untreated MM with higher frequency in HRD versus NHRD MM: 53% versus 28% (Misund, ASH 2016). No MYC SV were detected in MGUS cohort, SMM non-progressors at >5 years or SMM progressing between 2-5 years. By contrast, MYC SV were detected in 49% SMM that progressed within 2 years, 55% in HRD and 41% NHRD. SMM with MYC SV had a significantly shorter median TTP compared to patients without MYC SV (11.5 months vs 61 month; p<0.0001). Multivariate analysis with high risk genetic groups and biomarkers for progression (BMPCs >/=60% and FLC ratio 100) confirm MYC SV as an independent variable for progression to MM (hazard ratio=7, 95% confidence interval 3.6-13.7, p=0.00001).RAS and NFKB pathway mutations were observed with similar frequencies in MM and SMM progressing within 5 years of diagnosis, but with lower frequency in those not progressing by 5 years follow up, and were not observed in the MGUS cohort. A trend toward shorter TTP was observed in patients with RAS pathway mutations but did not reach statistical significance.ConclusionIn conclusion, we describe MYC translocations as a genetic marker of and likely cause of progression to MM that are absent in MGUS and SMM with TTP >2 years. In contrast MM and SMM early progressors (TTP <2 years) share a similar genetic landscape. Identification of MYC translocations at diagnosis of SMM predicts short TTP to MM, defining a novel ultra-high risk category that merits validation in prospective clinical trials. [Display omitted] DisclosuresKumar:Skyline: Honoraria; Celgene, Millennium/Takeda, Onyx, AbbVie, Janssen, Sanofi, Novartis, Amgen, Genentech, Merck, Oncopeptides, Roche, Skyline Diagnostics: Research Funding; Celgene, Millennium, BMS, Onyx, Janssen, Noxxon, AbbVie, Amgen, Merck, Oncopeptides, Skyline Diagnostics, Takeda: Consultancy. Dispenzieri:Celgene, Millenium, Pfizer, Janssen: Research Funding. Fonseca:Novartis: Consultancy; Merck: Consultancy; Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; AMGEN: Consultancy; Celgene Corporation: Consultancy, Research Funding; Sanofi: Consultancy; Mayo Clinic & Dr Fonseca: Patents & Royalties: Prognostication of myeloma via FISH, ~$2000/year; Jansen: Consultancy; Bristol-Myers Squibb: Consultancy; Bayer: Consultancy; Pharmacyclics: Consultancy; Takeda: Consultancy. Stewart:Bristol-Myers Squibb: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Roche: Consultancy; Amgen: Consultancy.

Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.

The Valais Blackneck goat is a Swiss goat breed with a characteristic coat color phenotype. Before the revision of the breed standard in 1938, 4 different color varieties of Valais goats were known. Besides Blackneck animals resembling the modern breed standard, the brown and white Copperneck goat, the white Capra Sempione, and the greyish Grüenochte comprised the historic Valais goats. The brown pigmentation of Copperneck goats had previously been traced back to an introgression of a mutant TYRP1 allele from Toggenburg goats. In the present study, we identified additional introgression events of distinct ASIP alleles causing the remaining 2 rare coat color patterns within the Valais Blackneck goat breed. We identified the introgression of the AWt allele from Appenzell or Saanen goats in white Capra Sempione goats. Similarly, introgression of the Apc allele from Peacock goats resulted in the greyish Grüenochte phenotype. These results demonstrate past hybridization events between breeds that are separated today. A perfect genotype-phenotype association in 393 Valais goats supported the causality of the genotyped variants for the different coat color phenotypes. Our study gives insights into the introgression of functionally relevant copy number variant (CNV) alleles controlling pigmentation between goat breeds with strikingly different coat color patterns.

Late-Onset Neonatal Hypocalcemia Due to Transient Hypoparathyroidism in Infant of Mother With COVID-19 at Delivery

Introduction: Neonatal hypocalcemia is an uncommon condition but clinical presentation can include severe manifestations such as neuromuscular irritability, tetany, seizure or cardiac conduction abnormalities that require prompt intervention to normalize calcium levels. To our knowledge there have been no reports of neonatal hypocalcemia following maternal SARS-CoV2 infection at the time of birth. Here we report a case of transient late-onset neonatal hypocalcemia complicated by maternal SARS-CoV-2 infection at the time of delivery.Clinical Case: A 13-day old full-term appropriate for gestational age female was born to an asymptomatic mother who tested positive for SARS-CoV2 at the time of delivery. Caretakers noticed minor twitching movements in the first few days of life that were progressively worsening. Initial ionized calcium was 0.6 mmol/L, and labs at time of transfer to our hospital were notable for total calcium of 5.5mg/dL(n 8.9–9.9), and ionized calcium of 0.67mmol/L (n 1.12–1.37 mmol/L). Calcium levels improved after she received IV calcium boluses and was started on continuous IV calcium infusion. Initial phosphorus was 8.3 mg/dL (n 3.2–7.4 mg/dL) and magnesium was 1.2 mg/dL (n 1.5–2.2 mg/dL), while intact PTH was inappropriately low at 12.2 pg/mL (n 10–65 pg/mL), and urine calcium to urine creatinine ratio was below the limits of assay detection (n <0.86), consistent with a diagnosis of neonatal hypoparathyroidism. The 25-hydroxy vitamin D was 11.1 ng/mL (n 30–100 ng/mL), which may have also been a contributing factor. She had no dysmorphic features on examination concerning for 22q deletion syndrome, and tested negative for SARS-CoV2. Chromosomal microarray did not reveal clinically relevant copy number alterations or areas of homozygosity. Calcium stabilized on enteral calcium carbonate, calcitriol, and cholecalciferol, and she was weaned off of all supplementation. Prior to discharge PTH recovered to 36.9 pg/ml with a calcium of 9.9 mg/dL, phosphorus 7.7 mg/dL, normal magnesium and 25-hydroxy vitamin D (31.3 ng/ml). She was discharged on Similac PM 60/40 formula to reduce her dietary phosphorus content, and 400 IU of cholecalciferol.Conclusions: Hypocalcemia in patients with severe COVID-19 is being increasingly reported. There is minimal data on the effect of perinatal SARS-CoV2 infections on neonatal health. While this report does not establish causation, expanding awareness of neonatal abnormalities following maternal SARS-CoV2 infection at delivery will help to recognize causal associations and improve patient care.

BMPR1A and SMAD4 mutations in juvenile polyposis syndrome: clinicopathological and genetic data from two congolese patients

BackgroundJuvenile polyposis syndrome (JPS) is a rare genetic disorder due to germline mutations in BMPR1A or in SMAD4 that are both tumor suppressor genes. The main clinical manifestation is the presence of multiple hamartomatous polyps preferentially located in gastrointestinal tract, mostly in colorectal site. The polyps can degenerate and lead to inherited malignant tumors. Materials and MethodsAmong 3157 patients with malignant and benign tumors diagnosed in Brazzaville teaching hospital, 43 persons with polyposis in colorectal tube were recruited. The positive diagnosis was based on endoscopic examination, World Health Organization and JASS guidelines clinical criteria, histopathological analysis and next-generationsequencing of DNAs extracted from peripheral blood of the patients. ResultsAmong 43 patients having polyposis, two were male patients identified with JPS representing 4.65% of polyposis and 0.06% of all tumors. Histological examination revealed typical JPS features. In those two males, whole genome comparative microarray did not identify relevant copy number imbalances. DNA sequencing of a comprehensive gene cancer genes panel identified specific mutations in the BMPR1A and SMAD4 genes. ConclusionWe have shown that BMPR1A and SMAD4 gene disorders are responsible for JPS in congolese patients as well and a novel mutation has been identified in one individual. As the condition predisposes highly to hereditary colorectal cancer, a comprehensive assessment of the JPS including genetic testing should be implemented in order to facilitate early diagnosis in Congo Brazzaville.

8. A partial deletion of the EP300 gene detected by microarray in an individual with mild autism

Current chromosomal microarray (CMA) methods identify deletions and duplications as small as ∼25 kilobases, thereby providing a useful test for clinically relevant copy number variants (CNVs). When a pathogenic CNV is identified by CMA, it is most often several hundred kilobases in size, encompassing multiple disease-associated genes. Here, we report a de novo 37 kilobase deletion of the terminal exons of the EP300 gene, detected by CMA in an individual with autism. The patient was a female diagnosed with mild autism as an adolescent; additional clinical indications included developmental delay, obesity, and congenital heart anomaly.