Added value of next generation gene panel analysis for patients with elevated methylmalonic acid and no clinical diagnosis following functional studies of vitamin B12 metabolism

Abstract Purpose Approximately 228,820 people are diagnosed annually with lung cancer diagnosis and 135,720 die from their disease1. EGFR and KRAS targeted therapies have been shown to significantly improve treatment of non-small cell lung cancer (NSCLC), but they don’t apply to the majority of patients. There’s a critical need to characterize the molecular signature of patients with lung cancer and to define the proportion of patients eligible for novel targeted therapies. Methods IRB approval was obtained to retrospectively extract data from tertiary hospital tumor registry from 2011 to 2017. Data collected included patient demographics, targeted next generation sequencing results (50 and 150 gene panel), histology, and biopsy location in the final 2,203 patients, 715 of which were manually checked. Findings 83.8% of patients in the lung cancer cohort that had targeted next-generation gene panel analysis demonstrated presence of at least one mutation. 50.9% of the patients in our cohort had a targetable mutation. There were 9.5% with hypermutated phenotype characterized as at least 5 mutations per sample. 1.3% of patients had at least 10 mutations per sample. We also characterize the distribution of mutations within brain metastatic lesions and demonstrate that brain metastases with hypermutated phenotype demonstrate larger volumes of edema and greater involvement of deep white matter than non-hypermutated brain metastases. Conclusion We present a comprehensive analysis of the molecular signature of lung cancer from a tertiary referral institution with focused analysis of brain metastases. Lung cancer brain metastases with greater than 5 mutations correspond to greater volume of edema and involvement of deep white matter.

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Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis

Journal of Molecular Diagnostics ◽

10.1016/j.jmoldx.2016.04.002 ◽

2016 ◽

Vol 18 (5) ◽

pp. 657-667 ◽

Cited By ~ 26

Author(s):

Laila C. Schenkel ◽

Jennifer Kerkhof ◽

Alan Stuart ◽

Jack Reilly ◽

Barry Eng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Sanger Sequencing ◽

Gene Panel ◽

Panel Analysis ◽

Combined Approach ◽

Next Generation ◽

Generation Sequencing ◽

Dependent Probe

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Next Generation Industrial IoT Digitalization for Traceability in Metal Manufacturing Industry: A Case Study of Industry 4.0

Electronics ◽

10.3390/electronics10050628 ◽

2021 ◽

Vol 10 (5) ◽

pp. 628

Author(s):

Michail J. Beliatis ◽

Kasper Jensen ◽

Lars Ellegaard ◽

Annabeth Aagaard ◽

Mirko Presser

Keyword(s):

Industry 4.0 ◽

Manufacturing Industry ◽

Careful Consideration ◽

Added Value ◽

Shop Floor ◽

Circuit Boards ◽

Next Generation ◽

Road Map ◽

Industrial Iot ◽

Production Cycles

This paper investigates digital traceability technologies taking careful consideration of the company’s needs to improve the traceability of products at the production of GPV Group as well as the efficiency and added value in their production cycles. GPV is primarily an electronics manufacturing service company (EMS) that manufactures electronic circuit boards, in addition to big metal products at their mechanics manufacturing sites. The company aims to embrace the next generation IoT technologies such as digital traceability in their internal supply chain at manufacturing sites in order to stay compatible with the Industry 4.0 requirements. In this paper, the capabilities of suitable digital traceability technologies are screened together with the actual GPV needs to determine if deployment of such technologies would benefit GPV shop floor operations and can solve the issues they face due to a lack of traceability. The traceability term refers to tracking the geolocation of products throughout the manufacturing steps and how that functionality can foster further optimization of the manufacturing processes. The paper focuses on comparing different IoT technologies and analyze their positive and negative attributes to identify a suitable technological solution for product traceability in the metal manufacturing industry. Finally, the paper proposes a suitable implementation road map for GPV, which can also be adopted from other metal manufacturing industries to deploy Industry 4.0 traceability at shop floor level.

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SAT0531 NEXT GENERATION SEQUENCING AND AUTOINFLAMMATORY SYNDROMES: CLINICAL AND GENETICAL CORRELATION ON AN ADULT POPULATION FROM A REFERRAL THIRD-CARE CENTRE

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.5067 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1223-1223

Author(s):

J. R. Marques Soares ◽

M. Antolin Mate ◽

E. Garcia Arumi ◽

E. Tizzano Ferrari ◽

S. Bujan Rivas

Keyword(s):

Next Generation Sequencing ◽

Genetic Data ◽

Clinical Suspicion ◽

Gene Panel ◽

Adult Patients ◽

Next Generation ◽

Related Gene ◽

Unknown Significance ◽

Level Hospital ◽

Generation Sequencing

Background:Systemic autoinflammatory diseases (sAID) are a group of conditions with recurrent episodes of inflammation in absence of infection or autoimmune response. Its physiopathology mainly lies on mono/poligenic mutations involving genes related to the innate immune system response. Next Generation Sequencing (NGS) platformss have been a big step forward on sAID diagnosis, although a clinical and genetic correlation is still needed.Objectives:To review the sAID related gene panel variants identified using NGS sAID gene panel on a cohort of adult patients screened for sAID from a referral third-level hospital.To correlate genetic and clinical findings for sAID related variants identified in order to the clinical suspicion diagnosis of sAID.Methods:A retrospective review of a cohort of adult (≥ 16 yo) patients with available NGS sAID related gene panel (MiSeq Illumina sequencing platform including intron and exon variants from up to 17 sAID genes, with coverage depth > x100) among 2014 and 2019 was performed.Demographic, clinical and genetic data were collected in a database.Genetic variants were classified according to the American College of Medical Genetics/Association for Molecular Pathology classification as benign/likely benign/variable of unknown significance (VUS)/likely pathogenic/pathogenic. In case of polymorphisms or lack of genetic data, the variants were named as unclassified.A description of the cohort and an analysis of the correlation assessment between clinical data and genetic findings were performed.Results:246 out of 299 (82%) patients with NGS sAID gene panel had clinical data available. 170/246 (69%) were adult patients. The medium age was 48 yo, and the M/F ratio was 2.46. 87/170 (51%) adult patients presented 122 variants involving sAID genes (60/87 patients with a single variant). All the variants out of 7 seven were heterozygous variants.Variants were classified according to ACMG/AMP as follow: pathogenic/probably pathogenic: 22/122 (18%), unknown significance: 74/122 (60.6%), benign/probably benign: 6/122 (4.91%). 20/122 (16.4%) were unclassified variants or polymorphisms.The most frequent variants identified involved MEFV (54/122), NOD2/CARD15 (18/122) and TNFRSF1A (17/122 including 12 p.Arg121Gln variants) genes.37/122 (30%) variants correlated with the clinical picture in 33 patients, allowing to confirm the suspected diagnosis. Among the 122 variants, 7 not previously communicated variants were identified.No somatic variants were found.Conclusion:NGS sAID related gene panel is a useful tool for sAID diagnosis. In this cohort of 170 adult patients from a referral third-level hospital, genetic tests identified sAID related variants in almost half of them.20% of patients who underwent genetic NGS sAID related gene panel studies were finally diagnosed with sAID.The identification of a genetic variant (even pathogenic / likely pathogenic variant) is not diagnostic for sAID if there is not a suggestive clinical picture.Despite genetic findings, a careful evaluation of clinical – genetic correlation is needed to confirm the suspicion diagnosis, especially for low penetrance variants like TNFRSF1A p. Arg121Gln.References:Diagnostic utility of a targeted next-generation sequencing gene panel in the clinical suspicion of systemic autoinflammatory diseases: a multi-center study. Karacan I, Balamir A, Uğurlu S, et al. . Rheumatol Int. 2019 May;39(5):911-919. doi: 10.1007/s00296-019-04252-5. Epub 2019 Feb 19.Disclosure of Interests:None declared

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Next generation sequencing-based gene panel tests for the management of solid tumors

Cancer Science ◽

10.1111/cas.13837 ◽

2018 ◽

Vol 110 (1) ◽

pp. 6-15 ◽

Cited By ~ 20

Author(s):

Masayuki Nagahashi ◽

Yoshifumi Shimada ◽

Hiroshi Ichikawa ◽

Hitoshi Kameyama ◽

Kazuaki Takabe ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Gene Panel ◽

Next Generation ◽

Generation Sequencing

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Next-generation panel sequencing identifies NF1 germline mutations in three patients with pheochromocytoma but no clinical diagnosis of neurofibromatosis type 1

Acta Endocrinologica ◽

10.1530/eje-17-0714 ◽

2018 ◽

Vol 178 (2) ◽

pp. K1-K9 ◽

Cited By ~ 12

Author(s):

Laura Gieldon ◽

Jimmy Rusdian Masjkur ◽

Susan Richter ◽

Roland Därr ◽

Marcos Lahera ◽

...

Keyword(s):

Genetic Analysis ◽

Thyroid Carcinoma ◽

Medullary Thyroid Carcinoma ◽

Clinical Diagnosis ◽

Neurofibromatosis Type 1 ◽

Neurofibromatosis Type ◽

Germline Mutations ◽

Next Generation ◽

Medullary Thyroid

Objective Our objective was to improve molecular diagnostics in patients with hereditary pheochromocytoma and paraganglioma (PPGL) by using next-generation sequencing (NGS) multi-gene panel analysis. Derived from this study, we here present three cases that were diagnosed with NF1 germline mutations but did not have a prior clinical diagnosis of neurofibromatosis type 1 (NF1). Design We performed genetic analysis of known tumor predisposition genes, including NF1, using a multi-gene NGS enrichment-based panel applied to a total of 1029 PPGL patients. We did not exclude genes known to cause clinically defined syndromes such as NF1 based on missing phenotypic expression as is commonly practiced. Methods Genetic analysis was performed using NGS (TruSight Cancer Panel/customized panel by Illumina) for analyzing patients’ blood and tumor samples. Validation was carried out by Sanger sequencing. Results Within our cohort, three patients, who were identified to carry pathogenic NF1 germline mutations, attracted attention, since none of the patients had a clinical suspicion of NF1 and one of them was initially suspected to have MEN2A syndrome due to co-occurrence of a medullary thyroid carcinoma. In these cases, one splice site, one stop and one frameshift mutation in NF1 were identified. Conclusions Since phenotypical presentation of NF1 is highly variable, we suggest analysis of the NF1 gene also in PPGL patients who do not meet diagnostic NF1 criteria. Co-occurrence of medullary thyroid carcinoma and PPGL was found to be a clinical decoy in NF1 diagnostics. These observations underline the value of multi-gene panel NGS for PPGL patients.

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Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2017-0046-oa ◽

2017 ◽

Vol 142 (3) ◽

pp. 353-357 ◽

Cited By ~ 12

Author(s):

Mitra Mehrad ◽

Somak Roy ◽

Humberto Trejo Bittar ◽

Sanja Dacic

Keyword(s):

Next Generation Sequencing ◽

Lung Adenocarcinoma ◽

Small Cell ◽

Gene Panel ◽

Next Generation ◽

Small Cell Lung ◽

Genomic Alterations ◽

Generation Sequencing ◽

Gene Alterations ◽

Cancer Panel

Context.— Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance. Objective.— To determine the best testing algorithm for patients with lung cancer in our clinical practice. Design.— Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel. Results.— Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations. Conclusions.— The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.

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The relationship between the cobalt nutrition of ewes and the vitamin B12 status of ewes and their lambs

Australian Journal of Agricultural Research ◽

10.1071/ar9871071 ◽

1987 ◽

Vol 38 (6) ◽

pp. 1071 ◽

Cited By ~ 19

Author(s):

MF Quirk ◽

BW Norton

Keyword(s):

Vitamin B12 ◽

Milk Production ◽

Acid Concentration ◽

Methylmalonic Acid ◽

Vitamin B12 Deficiency ◽

Lactation Performance ◽

Lower Productivity ◽

Cotton South ◽

B12 Deficiency ◽

The Relationship

An experiment was undertaken at Mt Cotton, south-east Queensland, to investigate the relationship between the cobalt nutrition of ewes and the occurrence of vitamin B12 deficiency in ewes and their lambs. Ewes received either no supplementary cobalt (C), 0.03 mg cobalt day-1 (LC), 0.06 mg cobalt day-1 (HC) or a cobalt bullet and grinder (CB). LC and HC ewes received their supplement as a weekly drench. Supplementation commenced prior to joining, and ewes subsequently grazed pangola grass pastures containing between 0.05 and 0.11 mg kg-1 cobalt.Cobalt supplementation of ewes increased their liveweight, reproductive and lactation performance. The milk production of ewes was influenced by the level of supplementation, with C, LC, HC and CB ewes producing 31.1, 41.5, 47.7 and 50.31. of milk respectively during the first 4 weeks of lactation. The lower productivity of C ewes was associated with concentrations of vitamin B12 in serum of less than 200 pg ml-1 and with the presence of detectable concentrations of methylmalonic acid (>80 8moles l-1) and formiminoglutamic acid (>30 8moles l-1) in their urine.The growth of lambs was influenced by the cobalt nutrition of their dams; the mean liveweight gain from birth to weaning (14 weeks of age) for lambs from C, LC, HC and CB ewes was 95, 158, 194 and 231 g day-1. Vitamin B12 deficiency was evident in lambs reared by C ewes from 4 weeks of age, but lambs from LC and HC ewes did not become deficient until 8 and 12 weeks of age respectively. Lambs from CB ewes remained free of signs of deficiency prior to weaning. Urinary formiminoglutamic acid concentration was a more reliable indicator of vitamin B12 status in young lambs than urinary methylmalonic acid concentration. The concentrations of vitamin B12 in the serum of lambs were low in all groups (< 150 pg ml-1) and were generally unaffected by the cobalt nutrition of their dams.A dietary cobalt intake of about 0.15 mg day-1 appeared to be necessary for optimal milk production from ewes. However, this level of dietary cobalt was inadequate for provision of sufficient quantities of maternal vitamin B12 to meet the requirements of lambs in the later stages of lactation.

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