IBM C9560-659 : Fundamentals of Applying IBM SmartCloud Control Desk V1 Exam
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IBM V1 test
Cholangiocarcinoma (CCA), a worldwide health issue, constitutes about 10%-20% of all primary liver cancers international. Geographic model in CCA incidence has been attributed to differing possibility components in the affected population. In Western countries, together with the us, metabolic syndrome, inflammatory bowel ailment, simple sclerosing cholangitis, hepatitis C, and alcohol abuse are the main CCA possibility factors, and the age-standardized incidence fee is 1.6 per one hundred,000.1 The incidence in Southeast Asia is extremely high, as much as seventy one.three per one hundred,000 in definite ingredients of Asia, and is associated with liver fluke and hepatitis B virus (HBV) infection.2
We in comparison the genomic landscape of intrahepatic cholangiocarcinoma in Asian and Western sufferers with this disorder the usage of next-era sequencing. These differences might also have therapeutic implications.
Asian patients harbored a higher rate of DNA restoration gene mutations compared with Western patients. Actionable driver gene adjustments were greater general in the Western sufferers. although, high tumor mutation burden (TMB) price (> 10 mut/Mb) turned into significantly more regular in Asian patients than in their Western counterparts. sufferers with excessive TMB had ameliorations in direct DNA repair genes and caretaker genes, particularly within the Asian population.
These consequences may additionally replicate variations in ailment etiology and are important for centered therapy and immunotherapy trials for sufferers with intrahepatic cholangiocarcinoma.
in particular, there is an increasing incidence of intrahepatic cholangiocarcinoma (IHCCA) international, and its etiology is uncertain.3 Surgical resection is the handiest probably curative medication, but the majority of patients latest with an superior disorder stage and have a limited therapeutic alternatives. recently, subsequent-era sequencing (NGS) has been hastily incorporated into the clinical management of CCA, particularly in the united states. IHCCA, in specific, is enriched with a relatively high variety of actionable mutations, and early reports point out several promising leads with targeted treatments for fibroblast increase factor receptor 2 fusion (FGFR), isocitrate dehydrogenase-1 (IDH1), BRAF V600E mutations, and HER2/neu amplification.2 nonetheless, NGS facts from Asia, where CCA is most established, are restricted. These records are critical toward building of targeted treatment options for this disease.
CCA genetic profiling studies have recognized genetic diversity between intrahepatic and extrahepatic subtypes. similarly, there seems to be genetic diversity between liver fluke and nonliver fluke–linked CCA in Asia.four during this look at, they explored the genomic heterogeneity of IHCCA between Asian and Western populations using a focused NGS platform.
complete genomic profiling of formalin-mounted paraffin-embedded (FFPE) tumor tissue blocks from the primary tumor or metastatic lesions received from sufferers with IHCCA become carried out in 283 patients from a single center within the u.s. and in 164 sufferers from China. within the u.s., all genomic profiling evaluation became carried out the usage of a scientific Laboratory growth Amendments (CLIA)-validated platform (basis medicine, Cambridge, MA). In China, genomic profiling changed into carried out by using one more CLIA-validated focused sequencing platform (OrigiMed, Shanghai, China).5 A bridging look at comparing the 2 systems indicated high concordance (96.three%; 26/27) for the same study samples (outcomes indicated in Appendix table A1). All study-enrolled patients signed a consent form enabling the free up of their tissue blocks to be confirmed. All FFPE tissue blocks were sectioned and stained with hematoxylin and eosin and reviewed by way of an expert pathologist to confirm the prognosis and presence of least 20% of the DNA derived from tumor cells. This analysis become accredited by means of the institutional assessment boards at MD Anderson cancer center and Peking Union medical college.
Hybrid preference and Sequencing
A customized hybridization seize panel including over 23,660 in my view synthesized 5′-biotinylated DNA 120 bp oligonucleotides changed into used to goal the exons of melanoma-related genes, as well as selected introns of genes commonly rearranged in melanoma. Hybridization trap adopted the protocol of Hybridization capture of DNA libraries the use of xGen Lockdown Probes and Reagents (version three; built-in DNA technologies, San Diego, CA). Postcapture libraries were mixed together, denatured, diluted, after which sequenced. For the goal of estimation of sequencing error fee, a PhiX spike-in turned into added as an external handle to measure the percentage of reads with 0-4 mismatches, following the system described by using Manley et al.6
every kind of genetic ameliorations, together with single-nucleotide variant (SNV), brief and lengthy indels, copy number transformations (CNAs), and gene rearrangement, have been called 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 response (PCR) duplicates elimination the use of MarkDuplicates algorithm from Picard (edition 1.forty seven; Cambridge, MA). native realignment and base great recalibration for SNVs have been carried out the usage of GATK (v3.1-1; Cambridge, MA) and because of this called by MUTECT (v1.7; Cambridge, MA). The CNAs protected: (1) amplification, described as an increase within the variety of gene segment copies by ≥ 8, and (2) homozygous deletion, defined as decrease of complete loss of gene segment copies in samples with > 20% purity. To establish these differences, tumor cellularity turned into estimated via allele frequencies of sequenced single-nucleotide polymorphisms (SNPs). For detection of gene rearrangement, aligned reads with abnormal insert dimension of > 2,000 or zero bp have been gathered and used as discordant reads, it is, paired-end reads that couldn't be carefully mapped to a genome reference, with each and every study of paired reads aligned to the same chromosomes or distinctive chromosomes. initially, the discordant reads with the gap under 500 bp shaped clusters were further assembled through fermi-lite to identify competencies rearrangement breakpoints. The breakpoints had been double tested through BLAT, and the ensuing chimeric gene candidates were annotated.
Oncogenic Genetic Mutations
Statistical evaluation became only in accordance with oncogenic genetic variants and the variations of unknown value; low-frequency (variant allele frequency < .01) variants had been excluded. Oncogenic standards included: (1) regularly occurring pathogenic: oncogenic mutations supported via selected functional reviews; (2) doubtless pathogenic: specific practical reports exist on the mutations based on the equal genome loci and structural disrupting mutations on tumor suppressor genes, akin to truncations, splicing sites, and frameshifts; (three) demonstrated somatic: somatic mutations recorded on the general public genomic database, corresponding to COSMIC, and detected as a minimum once in any tumor kinds.
Tumor Mutation Burden
Tumor mutation burden (TMB) was estimated for 157 US patients and 164 chinese language sufferers with IHCCA with the aid of counting its somatic mutations, together with coding SNVs and indels per megabase of the sequence examined. Driver mutations and conventional germline transformations in dbSNP have been no longer counted. They classified their patients in response to the TMB scores 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 (three) TMB excessive (TMB-H) if the variety of mutations per megabase became ≥ 10. The TMB cutoff changed into defined per prior lung cancer trials.7,eight
We decided the microsatellite instability (MSI) status in all sufferers with detectable TMB reputation. in response to the MSI score, they labeled the samples as MSI excessive (MSI-H), defined as instability in ≥ 2 microsatellite loci; MSI low, defined as instability in only 1 loci; and microsatellite solid, defined as absence of any facts of microsatellite loci instability. If the effects for a pattern had been ambiguous, the evaluation turned into performed a second time. PCR validation confirmed the prognosis of MSI-H.
Statistical analysis became carried out with IBM SPSS version 24.0 (SPSS, Armonk, ny). P values < .05 were regarded significant. They used χ2 verify or Fisher’s accurate test for specific variables and the Kruskal-Wallis check for continual variables. A field and whisker plot become performed to investigate the distribution of TMB amongst Western and Asian patients with IHCCA.
affected person qualities
The imply age and commonplace deviation was 59.6 ± 9.9 and 58.3 ± 12.5 years for the chinese language and US cohorts, respectively. among the many chinese language cohort, 61.6% have been male, with a tremendously better male-to-feminine ratio (1.6:1) compared with the USA cohort. although 74.2% of US patients have been White, fifty three (18.8%) of sufferers have been non-White, together with 20 (7.1%) Hispanics, 18 (6.four%) Asians, 14 (4.9%) Blacks, and 21 (7.5%) had been other. the majority of the patients had stage III and IV sickness, without a huge ameliorations between the USA (seventy seven%) and chinese language (seventy eight%) sufferers. although, there become a stronger proportion of sufferers with stage I and II ailment in the US and chinese language cohorts, respectively. The percent of HBV-tremendous sufferers had been larger in the chinese language cohort than within the US cohort. furthermore, the chinese language sufferers had a tremendously bigger cost of neatly-differentiated adenocarcinoma in comparison with their US counterparts (P = .002; table 1).
table 1. Demographics for chinese language and US sufferers With Intrahepatic Cholangiocarcinoma
Western Versus Asian NGS finished Genomic Profiling
comprehensive genomic profiling identified 1,007 genetic aberrations (fuel) in chinese patients compared with 971 gasoline in US sufferers (Appendix table A2). every patient harbored as a minimum 1 GA, with an average of 6.1 (range, 1 to approximately 20) and 3.4 (range, 1 to about 16) gasoline per tumor in chinese language and US sufferers, respectively. As indicated in figure 1, essentially the most frequently suggested gasoline in chinese language sufferers have been tumor protein fifty three (TP53; forty one.5%), Kirsten rat sarcoma viral oncogene homolog (KRAS; 28.7%), AT-wealthy 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; 13.4%). For the united states sufferers, they have been CDKN2A/B (30%), IDH1/2 (23.three%), TP53 (20.eight%), ARID1A (19.8%), and fibroblast growth aspect receptors FGFR1-four (17.7%). among the many chinese language sufferers, 118 (72.0%) had as a minimum 1 actionable GA, with a tremendously higher frequency in KMT2C, BRCA1/2, and DDR2 compared with US sufferers (P = .02, .003, and .003, respectively). within the US patients, 154 patients (60.9%) had at least 1 actionable GA, with enormously greater frequency of CDKN2A/B and IDH1/2 fuel (P = .0004 and < .001, respectively; desk 2; Fig 1)
desk 2. adaptations in the Genomic Aberrations among chinese language and US patients With Intrahepatic Cholangiocarcinoma
gasoline in nuclear factor kappa B pathway regulators and DNA restoration genes happened greater often in chinese sufferers (P = .006 and .001, respectively; Fig 2). In their cohorts, they defined DNA fix genes to encompass the 20 most widely wide-spread up to now mentioned DNA fix gene fuel, including direct DNA repair 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 language patients harbored extra DNA restore fuel compared with US sufferers with IHCCA, with predominant gasoline in TP53, BRCA1/2, KMT2C, and RAD50. fuel in BLM, POLD1, PRKDC, and SLX4 had been no longer identified in both cohort. (table 2; Fig 1)
additionally, in the chinese language cohort, 10.four% of patients had TMB-H, 13.four% had TMB-I, and seventy six.2% had TMB-L compared with 5.7% with TMB-H, 15.3% with TMB-I, and seventy nine% with TMB-L among US patients (P = .18, 0.45, and nil.65, respectively). in addition, there become no big change in the median values of TMB-H, TMB-I, and TMB-L corporations among the chinese (14, eight, and a couple of mut/Mb, respectively) and US sufferers with IHCCA (19, 7, and three mut/Mb, respectively). additionally, they identified that the cost of MSI-H in chinese and US patients changed into 1.8% (n = 3) and 0.6% (n = 1), respectively, and all MSI-H patients were linked to high TMB values (Fig 2).
We explored the association between DNA fix gene fuel and TMB, and identified a tremendously larger price of TMB-I and TMB-H in patients who had combined direct and caretaker DNA restore gasoline compared with sufferers with out DNA fix gasoline among the chinese (P < .001) and US (P = .05) patients with IHCCA. This was certainly high-quality with changes of both direct and caretaker DNA restoration gene alterations (desk three; Fig three).
desk 3. affiliation Between DNA fix gas and TMB amongst chinese language and US patients With Intrahepatic Cholangiocarcinoma
IHCCA is an aggressive ailment with limited remedy alternatives. The creation of NGS offers promising breakthroughs with targeted therapy and immunologic interventions. youngsters, it is crucial to establish genomic heterogeneity between populations as a result of this could have a significant have an impact on on precision drugs approaches for this cancer.
In their look at, they performed comprehensive molecular profiling of 164 chinese language and 283 US patients with IHCCA to explore genomic heterogeneity between populations. They mentioned crucial differences between Asian and Western patients with IHCCA. through the consequences, chinese sufferers had tremendously higher frequency of TP53 as well as KMT2C, BRCA1/2, DDR, TERT, TGFBR2, RBM10, NF1, SPTA1, and RB1 gas. in the Western cohort, gas in IDH1/2, BAP1, and CDKN2A/B were more dominant. This genetic variety may well be attributed to variations within the underlying sickness risk factors (desk 2). In Western countries, CCA is linked to metabolic syndrome, inflammatory bowel sickness, simple sclerosing cholangitis, and hepatolithiasis, whereas liver fluke and HBV are critical chance components in Asian international locations. A old analyze advised that fluke-related CCAs are enriched with ERBB2 amplification and TP53 mutation, whereas fluke-bad CCAs have a higher fee of IDH1/2, BAP1, FGFR/PRKA fuel, and programmed loss of life-1 (PD-1)/programmed dying-ligand 1 (PD-L1) expression.10,11 furthermore, in a fresh genetic profiling study of 103 chinese patients with IHCCA, it changed into noted that TP53 mutations have been extra commonly viewed in HBV-linked IHCCA, whereas KRAS mutation changed into extra possible happen in HBV-poor IHCCA.12
additionally, their facts demonstrated an universal excessive frequency of DNA repair gasoline: in 62.6% of chinese language sufferers and 45.9% of US sufferers. Dysregulation of DNA restore pathway is regularly associated with accumulation of several fuel and higher TMB. totally mutated tumors harbor neoantigens, which make them more responsive to immune checkpoint inhibitors. This has also been Tested in a old examine of lenvatinib with PD-1 inhibition for intrahepatic cholangiocarcinoma performed by their neighborhood. in this analyze, high TMB was associated with longer development-free survival.13 additionally, pembrolizumab has been accredited via the food and Drug Administration for the DNA mismatch fix deficient (MMR-d) cancers in line with a phase II medical trial that confirmed a 40% aim response price and 78% progression-free survival price in sufferers with colorectal melanoma with MMR-d in comparison with 0% and eleven%, respectively, for MMR-educated patients.14 equivalent outcomes had been accomplished in noncolorectal cancers that covered 4 sufferers (44%) with biliary tract melanoma. additionally, it has been identified that certain somatic mutations could lead to alteration within the immune biomarker expression. for example, BRCA1/2 mutated high-grade serous ovarian carcinoma had drastically higher CD3+ and CD8+ tumor infiltrating lymphocytes, in addition to elevated PD-1 and PD-L1 expression, in tumor-associated immune cells compared with tumors devoid of BRCA1/2 mutations.15,sixteen In their analyze, chinese language sufferers had significantly better BRCA1/2 fuel (8.5%) compared with Western sufferers (1.eight%).
We classified their sufferers in keeping with the TMB ranking, and they regarded TMB to be excessive if it turned into ≥ 10 mut/Mb in line with outcomes of the lately published CheckMate 568 trial that Tested 44% overall response rate in patients who had TMB ≥ 10 mut/Mb when handled with combined nivolumab and ipilimumab (no matter PD-L1 expression).7 In their study, a minority of sufferers with IHCCA had been TMB-H (12.2% and 5.9% in Asian and Western cohorts, respectively). moreover, a significant affiliation between DNA restore gasoline and TMB-H and TMB-I has been decided. The function of mixed poly (ADP-ribose) polymerase inhibitors and PD-1 inhibitors in advanced strong tumor is at present under investigation and may be relevant to this subgroup.
Our look at has crucial barriers. They obtained the comprehensive genetic alteration facts employing 2 focused gene panels. In these panels: (1) the content material genes had some dissimilarities; to address this difficulty, they filtered out differential genes and best covered the 320 overlapped genes into the analysis, thereby guaranteeing the comparability; (2) sequencing systems had been Illumina HiSeq2500 (Illumina, San Diego, CA) for FoundationOne and NovaSeq (Illumina) for OrigiMed450, with advantageous depths of 500× and seven hundred×, each reflecting the accuracy of sequencing results17; (3) the TMB algorithm of OrigiMed450 turned into according to the published algorithm of FoundationOne, and the genomic alterations were selected similarly18; (four) the OrigiMed450 platform uses blood samples from particular person sufferers as their own control for getting rid of the have an impact on of germline polymorphisms, whereas FoundationOne makes use of the somatic-germline-zygosity algorithm and databases of dbSNP and ExAC for a similar, and at last; and (5) they performed a bridging analyze evaluating the two structures and showed a excessive degree of concordance. regardless of these changes, they don't accept as true with that the consequences are affected in a meaningful method through the differing systems and are in step with prior stories. moreover, they now have examined the clinical features of the chinese language and US sufferers and tested that demographic transformations between these populations had been minor, with most patients having an advanced disorder stage. There became a more robust percentage of hepatitis B exposure within the Asian cohort, and the pathophysiologic relationship between the viral an infection and somatic mutations in cancer is unknown at present. Future reviews to examine the genomic profiling in different populations, making an allowance for the ailment chance elements, are warranted. information regarding PD-1 and PD-L1 expression have been not available; therefore, they could not establish adaptations in immune biomarker expression between the 2 cohorts in this analyze. To their talents, here is the primary analyze to examine genomic profiling adaptations between Asian and Western sufferers with IHCCA, and their records are more likely to be informative towards future precision medicine trials for this melanoma.
© 2020 with the aid of American Society of medical Oncology
Supported via department of defense provide No. CA180064.
conception 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 analyze substances or patients: Qiang Li, Jianzhen Lin, Lawrence N. Kwong, Haitao Zhao
assortment and assembly of data: 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
statistics 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
final approval of manuscript: All authors
liable for all features of the work: All authors
AUTHORS' DISCLOSURES OF knowledge CONFLICTS OF activity
here represents disclosure guidance offered through authors of this manuscript. All relationships are considered compensated except in any other case mentioned. Relationships are self-held unless cited. I = immediate family member, Inst = My institution. Relationships might also now not relate to the field rely of this manuscript. For extra counsel about ASCO's conflict of hobby coverage, please refer to www.asco.org/rwc or ascopubs.org/po/creator-center.
Open funds is a public database containing suggestions said via agencies about funds made to US-licensed physicians (Open funds).
Employment: MD Anderson melanoma middle
Honoraria: Sumitomo neighborhood, Dialectica
Consulting or Advisory role: Genentech, Inflection Biosciences, Pieris prescribed drugs, Clearlight Diagnostics, Darwin fitness, Samsung Bioepis, Spectrum pharmaceuticals, Aduro Biotech, OrigiMed, Xencor, Debiopharm group, Mersana, Seattle Genetics, Silverback Therapeutics, Immunomedics, IBM Watson fitness, F. Hoffman-LaRoche, IBM Watson health, PACT Pharma, Effector Therapeutics
speakers' Bureau: Chugai Biopharmaceuticals
analysis Funding: Novartis (Inst), AstraZeneca (Inst), Taiho Pharmaceutical (Inst), Genentech (Inst), Calithera Biosciences, Debiopharm neighborhood (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 health (Inst), Daiichi Sankyo (Inst), GlaxoSmithKline (Inst), Seattle Genetics (Inst)
shuttle, accommodations, fees: Taiho Pharmaceutical, Seattle Genetics, Beth Israel Deaconess clinical middle
Lawrence N. Kwong
stock and other ownership pastimes: Sarepta Therapeutics
analysis Funding: Array BioPharma
Mitesh J. Borad
stock and other ownership interests: Gilead Sciences, AVEO, Intercept prescription drugs, Spectrum prescription drugs
Consulting or Advisory function: G1 Therapeutics, Fujifilm (Inst), Agios (Inst), Insys Therapeutics (Inst), Novartis (Inst), ArQule (Inst), Celgene (Inst), Inspyr Therapeutics, Halozyme (Inst), Pieris pharmaceuticals (Inst), Taiho Pharmaceutical (Inst), Immunovative treatment options, Exelixis, Lynx neighborhood, Genentech, Western Oncolytics, Klus Pharma, Denovo, Merck, Imvax
analysis Funding: Boston Biomedical (Inst), miRNA Therapeutics (Inst), Senhwa Biosciences (Inst), MedImmune (Inst), BiolineRx (Inst), Agios (Inst), Halozyme (Inst), Celgene (Inst), Threshold prescribed drugs (Inst), Toray Industries (Inst), Dicerna (Inst), Sillajen (Inst), Eisai (Inst), Taiho Pharmaceutical (Inst), EMD Serono (Inst), Isis prescription drugs (Inst), Incyte (Inst), sun Biopharma (Inst), ARIAD (Inst), ImClone systems (Inst), QED Therapeutics (Inst), Incyte (Inst), Puma Biotechnology (Inst), Adaptimmune (Inst), Merck Serono (Inst), RedHill Biopharma (Inst), Basilea (Inst)
go back and forth, accommodations, prices: ArQule, Celgene, AstraZeneca
Consulting or Advisory function: Qed, Oncosil, Incyte, Mundi
other Relationship: Rafael prescription drugs, Incyte, Pieris prescription drugs, Merck, Merck Serono, Novartis, Seattle Genetics, BeiGene, QED Therapeutics, Bayer
No other talents conflicts of interest had been stated.
We recognized 10 patients who had been sequenced the use of the FoundationOne platform; of these, 7 with satisfactory cellularity were chosen for analysis. The revered blocks had been sectioned at 5 µm; the tumor content material dimension and were proven by means of a proficient pathologist, and at the least 5 unstained slides have been submitted for affirmation the use of the OrigiMed platform. Institutional review board approval become obtained for this analyze. A high diploma of concordance became referred to between the platforms, as indicated in table A1.
desk A1. influence of Actionable Alternation Between OrigiMed and FoundationOne Sequencing Platform
desk A2. finished Genomic Profiling recognized 1,007 gas in chinese language sufferers compared With US sufferers
Chun YS, Javle M: Systemic and adjuvant treatment plans for intrahepatic cholangiocarcinoma. cancer Contr 24:1073274817729241, 2017 Crossref, Google student2.
Jain A, Kwong LN, Javle M: Genomic profiling of biliary tract cancers and implications for clinical apply. Curr treat alternate options Oncol 17:58, 2016 Crossref, Medline, Google scholar3.
Saha SK, Zhu AX, Fuchs CS, et al: Forty-yr tendencies in cholangiocarcinoma incidence within the U.S.: Intrahepatic sickness on the upward thrust. Oncologist 21:594-599, 2016 Crossref, Medline, Google student4.
Ong CK, Subimerb C, Pairojkul C, et al: Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat Genet 44:690-693, 2012 Crossref, Medline, Google scholar5.
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