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IBM 000-923 : Netcool/Precision IP V3.6 Exam

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IBM V3.6 test prep

Intrahepatic Cholangiocarcinoma: Genomic Heterogeneity Between japanese and Western sufferers | 000-923 PDF get and Free test PDF

Cholangiocarcinoma (CCA), a worldwide fitness difficulty, constitutes about 10%-20% of all fundamental liver cancers international. Geographic model in CCA incidence has been attributed to differing possibility elements in the affected inhabitants. In Western international locations, together with the USA, metabolic syndrome, inflammatory bowel disease, primary sclerosing cholangitis, hepatitis C, and alcohol abuse are the leading CCA possibility factors, and the age-standardized incidence expense is 1.6 per a hundred,000.1 The incidence in Southeast Asia is extremely excessive, up to 71.3 per a hundred,000 in certain parts of Asia, and is linked to liver fluke and hepatitis B virus (HBV) infection.2

CONTEXT

  • Key purpose

  • We compared the genomic landscape of intrahepatic cholangiocarcinoma in Asian and Western sufferers with this disease the usage of subsequent-era sequencing. These alterations may additionally have therapeutic implications.

  • abilities Generated

  • Asian patients harbored a much better expense of DNA fix gene mutations compared with Western patients. Actionable driver gene ameliorations were more general in the Western patients. however, high tumor mutation burden (TMB) value (> 10 mut/Mb) changed into enormously extra typical in Asian patients than in their Western counterparts. patients with excessive TMB had ameliorations in direct DNA repair genes and caretaker genes, exceptionally within the Asian population.

  • Relevance

  • These consequences can also mirror changes in ailment etiology and are vital for focused remedy and immunotherapy trials for patients with intrahepatic cholangiocarcinoma.

  • primarily, there's an increasing incidence of intrahepatic cholangiocarcinoma (IHCCA) worldwide, and its etiology is uncertain.3 Surgical resection is the only potentially curative medicine, but the majority of patients existing with an advanced disease stage and have a constrained therapeutic alternatives. currently, subsequent-generation sequencing (NGS) has been rapidly integrated into the scientific management of CCA, principally in the u.s.. IHCCA, in selected, is enriched with a relatively excessive variety of actionable mutations, and early studies point out several promising leads with focused therapies for fibroblast increase factor receptor 2 fusion (FGFR), isocitrate dehydrogenase-1 (IDH1), BRAF V600E mutations, and HER2/neu amplification.2 even so, NGS records from Asia, the place CCA is most ordinary, are limited. These records are crucial towards construction of targeted healing procedures for this ailment.

    CCA genetic profiling studies have recognized genetic diversity between intrahepatic and extrahepatic subtypes. in a similar way, there seems to be genetic diversity between liver fluke and nonliver fluke–linked CCA in Asia.four in this study, they explored the genomic heterogeneity of IHCCA between Asian and Western populations using a targeted NGS platform.

    comprehensive genomic profiling of formalin-fastened paraffin-embedded (FFPE) tumor tissue blocks from the fundamental tumor or metastatic lesions acquired from patients with IHCCA changed into performed in 283 sufferers from a single middle in the united states and in 164 patients from China. within the united states, all genomic profiling evaluation become carried out the use of a scientific Laboratory growth Amendments (CLIA)-validated platform (basis medication, Cambridge, MA). In China, genomic profiling changed into performed by using an extra CLIA-validated focused sequencing platform (OrigiMed, Shanghai, China).5 A bridging study evaluating the two platforms indicated high concordance (ninety six.3%; 26/27) for the same study samples (outcomes indicated in Appendix desk A1). All examine-enrolled sufferers signed a consent kind permitting the free up of their tissue blocks to be established. All FFPE tissue blocks have been sectioned and stained with hematoxylin and eosin and reviewed by an authority pathologist to confirm the analysis and presence of least 20% of the DNA derived from tumor cells. This analysis become accredited with the aid of the institutional review boards at MD Anderson melanoma center and Peking Union clinical school.

    Hybrid option and Sequencing

    A customized hybridization seize panel including over 23,660 individually synthesized 5′-biotinylated DNA one hundred twenty bp oligonucleotides become used to goal the exons of cancer-connected genes, in addition to selected introns of genes frequently rearranged in melanoma. Hybridization trap followed the protocol of Hybridization capture of DNA libraries the usage of xGen Lockdown Probes and Reagents (edition 3; integrated DNA applied sciences, San Diego, CA). Postcapture libraries have been combined collectively, denatured, diluted, and then sequenced. For the aim of estimation of sequencing error fee, a PhiX spike-in become introduced as an external handle to measure the percent of reads with 0-four mismatches, following the components described with the aid of Manley et al.6

    Bioinformatics Pipeline

    all kinds of genetic variations, including single-nucleotide variant (SNV), short and lengthy indels, replica quantity changes (CNAs), and gene rearrangement, were referred to as the use of a collection of bioinformatics pipelines.5 evaluation of SNVs and indels begun with the alignment of uncooked reads to the human genome reference sequence (hg19) with the Burrows-Wheeler Aligner (v0.62; BWA, Cambridge, MA), adopted by means of polymerase chain reaction (PCR) duplicates removing the usage of MarkDuplicates algorithm from Picard (edition 1.47; Cambridge, MA). native realignment and base excellent recalibration for SNVs have been performed the usage of GATK (v3.1-1; Cambridge, MA) and as a result known as through MUTECT (v1.7; Cambridge, MA). The CNAs blanketed: (1) amplification, defined as an increase within the variety of gene section copies via ≥ 8, and (2) homozygous deletion, defined as lower of comprehensive lack of gene section copies in samples with > 20% purity. To determine these transformations, tumor cellularity become estimated by means of allele frequencies of sequenced single-nucleotide polymorphisms (SNPs). For detection of gene rearrangement, aligned reads with abnormal insert size of > 2,000 or zero bp were collected and used as discordant reads, it really is, paired-conclusion reads that could not be intently mapped to a genome reference, with each examine of paired reads aligned to the same chromosomes or diverse chromosomes. initially, the discordant reads with the space lower than 500 bp shaped clusters were further assembled through fermi-lite to identify knowledge rearrangement breakpoints. The breakpoints were double proven with the aid of BLAT, and the ensuing chimeric gene candidates had been annotated.

    Oncogenic Genetic Mutations

    Statistical analysis turned into simplest in keeping with oncogenic genetic variations and the variants of unknown magnitude; low-frequency (variant allele frequency < .01) variants had been excluded. Oncogenic standards protected: (1) widely used pathogenic: oncogenic mutations supported via particular practical reviews; (2) seemingly pathogenic: specific purposeful stories exist on the mutations headquartered on the same genome loci and structural disrupting mutations on tumor suppressor genes, akin to truncations, splicing websites, and frameshifts; (3) confirmed somatic: somatic mutations recorded on the public genomic database, similar to COSMIC, and detected at the least once in any tumor varieties.

    Tumor Mutation Burden

    Tumor mutation burden (TMB) turned into estimated for 157 US sufferers and 164 chinese patients with IHCCA by using counting its somatic mutations, including coding SNVs and indels per megabase of the sequence examined. Driver mutations and known germline ameliorations in dbSNP have been now not counted. They categorized their patients based on the TMB ratings into: (1) TMB low (TMB-L) if the variety of mutations per megabase (mut/Mb) changed into < 6, (2) TMB intermediate (TMB-I) if the variety of mutations per megabase become between 6 and 9, and (3) TMB high (TMB-H) if the variety of mutations per megabase was ≥ 10. The TMB cutoff changed into described per prior lung cancer trials.7,eight

    Microsatellite Instability

    We determined the microsatellite instability (MSI) status in all sufferers with detectable TMB reputation. in keeping with the MSI ranking, they categorised the samples as MSI high (MSI-H), defined as instability in ≥ 2 microsatellite loci; MSI low, described as instability in barely 1 loci; and microsatellite reliable, described as absence of any evidence of microsatellite loci instability. If the outcomes for a demo were ambiguous, the evaluation turned into performed a 2nd time. PCR validation proven the prognosis of MSI-H.

    Statistical analysis

    Statistical evaluation turned into performed with IBM SPSS version 24.0 (SPSS, Armonk, new york). P values < .05 were considered huge. They used χ2 examine or Fisher’s genuine look at various for express variables and the Kruskal-Wallis check for continuous variables. A container and whisker plot changed into performed to examine the distribution of TMB amongst Western and Asian patients with IHCCA.

    patient traits

    The mean age and commonplace deviation become fifty nine.6 ± 9.9 and fifty eight.3 ± 12.5 years for the chinese and US cohorts, respectively. among the chinese language cohort, 61.6% were male, with a greatly bigger male-to-feminine ratio (1.6:1) in comparison with the USA cohort. although seventy four.2% of US sufferers were White, fifty three (18.eight%) of sufferers were non-White, together with 20 (7.1%) Hispanics, 18 (6.4%) Asians, 14 (4.9%) Blacks, and 21 (7.5%) had been other. nearly all of the patients had stage III and IV ailment, with out a huge changes between the us (77%) and chinese language (78%) sufferers. youngsters, there changed into a higher proportion of sufferers with stage I and II disorder within the US and chinese language cohorts, respectively. The percentage of HBV-positive patients had been bigger in the chinese language cohort than in the US cohort. moreover, the chinese sufferers had a drastically higher price of neatly-differentiated adenocarcinoma in comparison with their US counterparts (P = .002; table 1).

    Table

    table 1. Demographics for chinese language and US sufferers With Intrahepatic Cholangiocarcinoma

    Western Versus Asian NGS complete Genomic Profiling

    complete genomic profiling recognized 1,007 genetic aberrations (gas) in chinese sufferers compared with 971 fuel in US patients (Appendix desk A2). each affected person harbored at the least 1 GA, with a normal of 6.1 (range, 1 to about 20) and three.four (range, 1 to about sixteen) gasoline per tumor in chinese language and US patients, respectively. As indicated in figure 1, essentially the most generally said fuel in chinese sufferers were tumor protein 53 (TP53; forty one.5%), Kirsten rat sarcoma viral oncogene homolog (KRAS; 28.7%), AT-rich interactive area-containing protein 1A (ARID1A; 18.3%), cyclin-based kinase inhibitor 2A and 2B (CDKN2A/B; 15.2%), and isocitrate dehydrogenase 1 and a couple of (IDH1/2; 13.four%). For the USA sufferers, they have been CDKN2A/B (30%), IDH1/2 (23.three%), TP53 (20.8%), ARID1A (19.eight%), and fibroblast growth element receptors FGFR1-four (17.7%). among the chinese patients, 118 (72.0%) had at least 1 actionable GA, with a tremendously greater frequency in KMT2C, BRCA1/2, and DDR2 compared with US sufferers (P = .02, .003, and .003, respectively). in the US patients, 154 sufferers (60.9%) had as a minimum 1 actionable GA, with vastly better frequency of CDKN2A/B and IDH1/2 gasoline (P = .0004 and < .001, respectively; desk 2; Fig 1)

    Table

    table 2. adaptations within the Genomic Aberrations among chinese and US sufferers With Intrahepatic Cholangiocarcinoma

    fuel in nuclear element kappa B pathway regulators and DNA restoration genes occurred greater generally in chinese patients (P = .006 and .001, respectively; Fig 2). In their cohorts, they defined DNA fix genes to consist of the 20 most conventional in the past suggested DNA repair gene gas, together with direct DNA restore genes (ATM, ATR, BRCA1, BRCA2, FANCA, FANCD2, MLH1, MSH2, MSH6, PALB2, POLD1, POLE, PRKDC, RAD50, and SLX4) and caretaker genes (BAP1, CDK12, KMT2C/MLL3, TP53, and BLM).9 Remarkably, chinese patients harbored more DNA repair gasoline compared with US patients with IHCCA, with predominant gas in TP53, BRCA1/2, KMT2C, and RAD50. gasoline in BLM, POLD1, PRKDC, and SLX4 have been no longer identified in both cohort. (table 2; Fig 1)

    moreover, in the chinese language cohort, 10.four% of patients had TMB-H, 13.4% had TMB-I, and 76.2% had TMB-L in comparison with 5.7% with TMB-H, 15.three% with TMB-I, and 79% with TMB-L among US sufferers (P = .18, 0.forty five, and zero.65, respectively). additionally, there become no giant change within the median values of TMB-H, TMB-I, and TMB-L businesses among the many chinese language (14, eight, and a pair of mut/Mb, respectively) and US patients with IHCCA (19, 7, and three mut/Mb, respectively). in addition, they recognized that the price of MSI-H in chinese and US patients become 1.8% (n = 3) and zero.6% (n = 1), respectively, and all MSI-H patients were associated with excessive TMB values (Fig 2).

    We explored the association between DNA restoration gene gas and TMB, and recognized a greatly bigger rate of TMB-I and TMB-H in sufferers who had mixed direct and caretaker DNA restoration gasoline in comparison with patients without DNA restoration fuel among the chinese language (P < .001) and US (P = .05) patients with IHCCA. This became principally exceptional with variations of each direct and caretaker DNA fix gene modifications (desk three; Fig three).

    Table

    table 3. association Between DNA fix gasoline and TMB among chinese language and US patients With Intrahepatic Cholangiocarcinoma

    IHCCA is an aggressive disease with restricted treatment alternate options. The creation of NGS offers promising breakthroughs with targeted remedy and immunologic interventions. although, it's vital to establish genomic heterogeneity between populations because this may have a major influence on precision drugs methods for this cancer.

    In their look at, they performed finished molecular profiling of 164 chinese and 283 US sufferers with IHCCA to explore genomic heterogeneity between populations. They stated critical adjustments between Asian and Western patients with IHCCA. throughout the effects, chinese language patients had enormously larger frequency of TP53 as well as KMT2C, BRCA1/2, DDR, TERT, TGFBR2, RBM10, NF1, SPTA1, and RB1 gasoline. in the Western cohort, fuel in IDH1/2, BAP1, and CDKN2A/B were greater dominant. This genetic variety may be attributed to variations in the underlying disorder chance components (table 2). In Western nations, CCA is linked to metabolic syndrome, inflammatory bowel disease, primary sclerosing cholangitis, and hepatolithiasis, whereas liver fluke and HBV are critical chance factors in Asian countries. A outdated examine advised that fluke-related CCAs are enriched with ERBB2 amplification and TP53 mutation, whereas fluke-poor CCAs have a higher cost of IDH1/2, BAP1, FGFR/PRKA gas, and programmed loss of life-1 (PD-1)/programmed loss of life-ligand 1 (PD-L1) expression.10,eleven in addition, in a fresh genetic profiling study of 103 chinese sufferers with IHCCA, it changed into mentioned that TP53 mutations have been more frequently considered in HBV-related IHCCA, whereas KRAS mutation changed into greater likely turn up in HBV-negative IHCCA.12

    moreover, their information demonstrated an universal high frequency of DNA repair gasoline: in sixty two.6% of chinese sufferers and 45.9% of US sufferers. Dysregulation of DNA restoration pathway is often linked to accumulation of several gas and higher TMB. highly mutated tumors harbor neoantigens, which make them more aware of immune checkpoint inhibitors. This has also been tested in a previous examine of lenvatinib with PD-1 inhibition for intrahepatic cholangiocarcinoma conducted through their community. in this analyze, excessive TMB turned into associated with longer development-free survival.13 additionally, pembrolizumab has been authorized via the food and Drug Administration for the DNA mismatch fix poor (MMR-d) cancers based on a part II clinical trial that confirmed a forty% aim response fee and seventy eight% development-free survival fee in patients with colorectal cancer with MMR-d compared with 0% and eleven%, respectively, for MMR-trained patients.14 similar outcomes have been finished in noncolorectal cancers that protected four sufferers (forty four%) with biliary tract melanoma. in addition, it has been recognized that selected somatic mutations may lead to alteration within the immune biomarker expression. as an instance, BRCA1/2 mutated excessive-grade serous ovarian carcinoma had significantly greater CD3+ and CD8+ tumor infiltrating lymphocytes, in addition to increased PD-1 and PD-L1 expression, in tumor-linked immune cells compared with tumors devoid of BRCA1/2 mutations.15,16 In their examine, chinese language patients had drastically higher BRCA1/2 fuel (8.5%) in comparison with Western sufferers (1.8%).

    We labeled their patients in line with the TMB rating, and they regarded TMB to be high if it was ≥ 10 mut/Mb according to consequences of the these days posted CheckMate 568 trial that demonstrated 44% normal response expense in sufferers who had TMB ≥ 10 mut/Mb when treated with mixed nivolumab and ipilimumab (no matter PD-L1 expression).7 In their study, a minority of sufferers with IHCCA were TMB-H (12.2% and 5.9% in Asian and Western cohorts, respectively). moreover, a significant association between DNA fix gas and TMB-H and TMB-I has been decided. The function of mixed poly (ADP-ribose) polymerase inhibitors and PD-1 inhibitors in superior solid tumor is at the moment under investigation and might be relevant to this subgroup.

    Our study has vital boundaries. They acquired the comprehensive genetic alteration records using 2 targeted gene panels. In these panels: (1) the content material genes had some dissimilarities; to tackle this challenge, they filtered out differential genes and best protected the 320 overlapped genes into the evaluation, thereby making certain the comparability; (2) sequencing structures had been Illumina HiSeq2500 (Illumina, San Diego, CA) for FoundationOne and NovaSeq (Illumina) for OrigiMed450, with effective depths of 500× and seven-hundred×, each reflecting the accuracy of sequencing results17; (three) the TMB algorithm of OrigiMed450 was in keeping with the posted algorithm of FoundationOne, and the genomic variations were chosen similarly18; (four) the OrigiMed450 platform makes use of blood samples from particular person sufferers as their personal handle for doing away with the impact of germline polymorphisms, whereas FoundationOne makes use of the somatic-germline-zygosity algorithm and databases of dbSNP and ExAC for a similar, and eventually; and (5) they carried out a bridging look at comparing the two platforms and confirmed a excessive diploma of concordance. despite these alterations, they do not accept as true with that the outcomes are affected in a significant method via the differing platforms and are consistent with past reviews. in addition, they now have examined the clinical traits of the chinese language and US patients and proven that demographic variations between these populations have been minor, with most patients having an superior disease stage. There became a more robust proportion of hepatitis B exposure in the Asian cohort, and the pathophysiologic relationship between the viral infection and somatic mutations in melanoma is unknown at this time. Future stories to examine the genomic profiling in diverse populations, taking into account the sickness risk factors, are warranted. facts related to PD-1 and PD-L1 expression had been now not purchasable; for this reason, they could not determine adaptations in immune biomarker expression between the 2 cohorts in this study. To their advantage, here is the first look at to examine genomic profiling diversifications between Asian and Western sufferers with IHCCA, and their facts are likely to be informative towards future precision medicine trials for this melanoma.

    © 2020 with the aid of American Society of scientific Oncology help

    Supported with the aid of branch of defense provide No. CA180064.

    theory and design: Siqin Liu, Reham Abdel-Wahab, Junjie Xu, Qiang Li, Jinwei Hu, Mitesh J. Borad, Kai Wang, Milind Javle, Haitao Zhao

    Administrative support: Jingyu Cao, Jing Hu, Maolin Yan

    Provision of study substances or sufferers: Qiang Li, Jianzhen Lin, Lawrence N. Kwong, Haitao Zhao

    assortment and meeting of statistics: Jingyu Cao, Jing Hu, Siqin Liu, Reham Abdel-Wahab, Qiang Li, Maolin Yan, Yujie Feng, Jianzhen Lin, Lawrence N. Kwong, Jinwei Hu, Fernando Carapeto, Milind Javle, Haitao Zhao

    records analysis and interpretation: Siqin Liu, Funda Meric-Bernstam, Reham Abdel-Wahab, Qiang Li, Songhui Zhao, Jian Wang, Lawrence N. Kwong, Jinwei Hu, Mitesh J. Borad, Milind Javle

    Manuscript writing: All authors

    closing approval of manuscript: All authors

    responsible for all elements of the work: All authors

    AUTHORS' DISCLOSURES OF advantage CONFLICTS OF interest

    here represents disclosure assistance offered by way of authors of this manuscript. All relationships are considered compensated until otherwise cited. Relationships are self-held unless mentioned. I = immediate family member, Inst = My institution. Relationships may additionally now not relate to the subject rely of this manuscript. For more information about ASCO's conflict of pastime policy, please seek advice from www.asco.org/rwc or ascopubs.org/po/author-middle.

    Open funds is a public database containing tips suggested via corporations about payments made to US-licensed physicians (Open payments).

    Funda Meric-Bernstam

    Employment: MD Anderson cancer core

    Honoraria: Sumitomo community, Dialectica

    Consulting or Advisory function: Genentech, Inflection Biosciences, Pieris prescription drugs, Clearlight Diagnostics, Darwin health, Samsung Bioepis, Spectrum pharmaceuticals, Aduro Biotech, OrigiMed, Xencor, Debiopharm neighborhood, Mersana, Seattle Genetics, Silverback Therapeutics, Immunomedics, IBM Watson health, F. Hoffman-LaRoche, IBM Watson fitness, PACT Pharma, Effector Therapeutics

    speakers' Bureau: Chugai Biopharmaceuticals

    research Funding: Novartis (Inst), AstraZeneca (Inst), Taiho Pharmaceutical (Inst), Genentech (Inst), Calithera Biosciences, Debiopharm group (Inst), Bayer (Inst), Aileron Therapeutics (Inst), PUMA Biotechnology (Inst), CytomX Therapeutics (Inst), Jounce Therapeutics (Inst), Zymeworks (Inst), Curis (Inst), Pfizer (Inst), Effector Therapeutics (Inst), AbbVie (Inst), Boehringer Ingelheim (I), Guardant fitness (Inst), Daiichi Sankyo (Inst), GlaxoSmithKline (Inst), Seattle Genetics (Inst)

    trip, accommodations, prices: Taiho Pharmaceutical, Seattle Genetics, Beth Israel Deaconess clinical core

    Songhui Zhao

    Employment: OrigiMed

    Lawrence N. Kwong

    inventory and other ownership pursuits: Sarepta Therapeutics

    research Funding: Array BioPharma

    Mitesh J. Borad

    stock and other possession pursuits: Gilead Sciences, AVEO, Intercept prescribed drugs, Spectrum pharmaceuticals

    Consulting or Advisory position: G1 Therapeutics, Fujifilm (Inst), Agios (Inst), Insys Therapeutics (Inst), Novartis (Inst), ArQule (Inst), Celgene (Inst), Inspyr Therapeutics, Halozyme (Inst), Pieris prescription drugs (Inst), Taiho Pharmaceutical (Inst), Immunovative healing procedures, Exelixis, Lynx group, Genentech, Western Oncolytics, Klus Pharma, Denovo, Merck, Imvax

    research Funding: Boston Biomedical (Inst), miRNA Therapeutics (Inst), Senhwa Biosciences (Inst), MedImmune (Inst), BiolineRx (Inst), Agios (Inst), Halozyme (Inst), Celgene (Inst), Threshold prescription drugs (Inst), Toray Industries (Inst), Dicerna (Inst), Sillajen (Inst), Eisai (Inst), Taiho Pharmaceutical (Inst), EMD Serono (Inst), Isis prescribed drugs (Inst), Incyte (Inst), solar Biopharma (Inst), ARIAD (Inst), ImClone methods (Inst), QED Therapeutics (Inst), Incyte (Inst), Puma Biotechnology (Inst), Adaptimmune (Inst), Merck Serono (Inst), RedHill Biopharma (Inst), Basilea (Inst)

    shuttle, lodgings, costs: ArQule, Celgene, AstraZeneca

    Kai Wang

    Employment: OrigiMed

    leadership: OrigiMed

    Milind Javle

    Consulting or Advisory position: Qed, Oncosil, Incyte, Mundi

    different Relationship: Rafael prescription drugs, Incyte, Pieris prescription drugs, Merck, Merck Serono, Novartis, Seattle Genetics, BeiGene, QED Therapeutics, Bayer

    No different advantage conflicts of activity have been said.

    methods

    We recognized 10 sufferers who had been sequenced using the FoundationOne platform; of these, 7 with ample cellularity had been chosen for analysis. The respected blocks were sectioned at 5 µm; the tumor content material measurement and were confirmed by means of a educated pathologist, and at least 5 unstained slides have been submitted for affirmation the use of the OrigiMed platform. Institutional overview board approval turned into got for this study. A excessive degree of concordance became referred to between the structures, as indicated in table A1.

    Table

    desk A1. outcomes of Actionable Alternation Between OrigiMed and FoundationOne Sequencing Platform

    Table

    desk A2. complete Genomic Profiling identified 1,007 fuel in chinese sufferers in comparison With US sufferers

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