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This abstraction included 12 patients diagnosed with cholangiocarcinoma (n = 2; case #1 and #3), gallbladder blight (n = 1; case #2), pancreatic blight (n = 1; case #4), or non-small corpuscle lung blight (n = 8; case #5–12) at our institute. Informed accord was acquired from all patients. This abstraction was accustomed by the Institutional Analysis Board of analytic assay and genome assay board at Yamanashi Central Hospital (G-2018-1) and complied with Acknowledgment of Helsinki principles. All borderline claret samples were taken afore biopsy, operation and assay test from patients who did not accustomed any treatment. Borderline claret samples were calm in EDTA-2Na absolute tube (Terumo, Tokyo, Japan) and centrifuged aural 2 hours afterwards accession claret at 820 × g at 25 °C for 10 min, and buffy coats were isolated. Supernatants were centrifuged at 20,000 × g at 25 °C for 10 min to abolish debris. Buffy covering and claret were stored at −80 °C until DNA extraction. Bump tissues were acquired by surgically resected tissues (n = 9; case #3 and #5–12), biopsies (n = 2; case #1 and #2) and assay (n = 1; case #4). All bump tissues and biopsy samples were anchored with 10% aloof buffered formalin and paraffin-embedded. Cytological specimens were anchored with 95% booze and decrepit with Papanicolau staining as ahead described13.
For consecutive concoction analysis, we acclimated EGFR Multiplex cfDNA Advertence Accepted Set (Horizon Discovery, Cambridge, UK) harboring engineered mutations. The mixtures represented 0.1%, 0.25%, 0.5%, 1%, 2.5% and 5% VAF range. The absolute cardinal of DNA absorption was kept in connected (20 ng/µl).
Buffy covering DNA abstraction was performed application the QIAamp DNA Claret Mini QIAcube Kit (Qiagen, Hilden, Germany) with the QIAcube (Qiagen) as ahead described14,15. Briefly, 200 μL of buffy covering was incubated with Protease K and absorber AL. Genomic DNA was apprenticed to the column, ablution with Absorber AW1 and AW2, and eluted with Absorber AE. The absorption of DNA was bent application the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Plasma DNA was extracted application the MagMAX Cell-Free DNA abreast kit (Thermo Fisher Scientific) with KingFisher Duo Prime (Thermo Fisher Scientific) as ahead described16. Briefly, 2–4 mL of claret was alloyed with Lysis/binding band-aid and alluring beads. Chaplet were done with Ablution band-aid and 80% ethanol. Claret DNA was eluted with 50 μL of Elution Buffer. The claret DNA absorption was bent with the Qubit dsDNA HS Assay Kit and Qubit 3.0 Fluorometer (Thermo Fisher Scientific) in accordance with the manufacturer’s instructions.
Serial sections 10-μm-thick were able from FFPE tissues of surgical and biopsy specimens application Arcuturus PEN Membrane Bottle Slides (Thermo Fisher Scientific)17. The sections were again deparaffinized and decrepit with hematoxylin-eosin. All slides were advised by a pathologist (T.O.) and cytotechnologist (K.A.) to assay cellular agreeable and characteristics as ahead described13 (Supplemental Table 1). Laser-capture microdissection was performed application an Arcturus XT laser microdissection arrangement (Thermo Fisher Scientific).
To access archival cytological specimen, the bottle slides was blood-soaked absorbed in xylene to abolish the awning glass. Application a razor blade, we anon aching bump beef from the absolute slide. Bump beef were calm into the antiseptic tube. DNA from surgical, biopsy specimens and cytological case extracted with the GeneRead DNA FFPE Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions. FFPE DNA was advised with uracil DNA glycosylase aural the kit. To appraise the affection and absorption of FFPE DNA, we acclimated the TaqMan RNase P Detection Reagents Kit and the FFPE DNA QC Assay v2 on a ViiA 7 Real-Time PCR Arrangement (Thermo Fisher Scientific) as ahead described13.
We fabricated four centralized panels targeting biliary-pancreatic- or lung cancer-associated genes for Non-MB and MB sequencing. The Ion AmpliSeq album set (Non-MB technology) and Ion AmpliSeq HD album set (MB technology) were advised on Ion AmpliSeq Designer (Thermo Fisher Scientific). Amplicon breadth was advised to be short, because FFPE DNA is abject during the fixation with formalin. Similarly, plsma DNA is burst to an almost breadth of ~170 bp in claret circulation18,19. We advised the average admeasurement of PCR amplicons of the Non-MB and MB biliary-pancreatic panels as 112 bp (range: 61–137) and 118 bp (range: 72–133), respectively. The average sizes of amplicons of the Non-MB and MB lung blight panels were 113 bp (range: 60–140 bp) and 117 bp (range: 75–135 bp), respectively.
The Non-MB-based biliary-pancreatic console targeting 60 genes including accomplished exons and hotspots independent 2,820 album pairs and spanned 280.22 kb (Table 1). To accomplish high-depth abstracts by MB sequencing analysis, genes and hotspot regions of absorption were selected. The MB-based biliary-pancreatic console targeting 21 genes independent 67 album pairs and spanned 7.22 kb. The Non-MB-based lung blight console was acclimated as ahead described16,18,20,21,22,23,24. The MB-based lung blight console targeted 17 genes absolute 62 album pairs and spanned 6.4 kb (Table 1). The absolute exons of TP53 were covered by both the MB-based biliary-pancreatic and lung panels.
We searched the abstract and alleged genes based on the afterward criteria: (a) decidedly mutated genes about to the accomplishments alteration ante analyzed by MutSigCV assay tool; (b) genes complex in signaling pathways and abeyant ameliorative targets in biliary-pancreatic or lung cancers; and (c) accepted disciplinarian genes or bump suppressor genes appear by TCGA25,26 and addition assay institute27,28,29,30,31,32. We advised the hotspot alteration armpit of anniversary gene from the Catalogue Of Actual Mutations In Blight (COSMIC) database33. Based on these antecedent data, we analyzed frequently mutated genes and accepted actual variants application tumor-normal brace samples.
Targeted sequencing was performed as ahead described23,34,35,36,37. Multiplex PCR was performed application the Ion AmpliSeq Library Kit Plus and Ion AmpliSeq album (Thermo Fisher Scientific) at 99 °C for 2 min, followed by 14–18 cycles of 99 °C for 15 s and 60 °C for 4 min, with a final authority at 10 °C. Album sequences were partially digested with FuPa reagent at 50 °C for 10 min, followed by 55 °C for 10 min and 60 °C for 20 min. Adaptor and barcode articulation was performed application Ion Xpress Barcode Adapters at 22 °C for 30–60 min, 68 °C for 5 min, 72 °C for 5 min and authority at 10 °C.
Multiplex PCR was performed with Ion AmpliSeq HD album and Ion AmpliSeq HD Library Kit (Thermo Fisher Scientific) in accordance with the manufacturer’s instruction. Album sets comprised two altered album pools. The acknowledgment admixture comprised 3.7 μL of 4x Amplification Mix, 1.5 μL of 10x advanced album mix, 1.5 μL of 10x about-face album mix, 1–20 ng of FFPE or claret DNA, and nuclease-free baptize up to 15 μL of absolute volume. PCR was performed to amplify the ambition regions with the afterward cycling conditions: three cycles of 99 °C for 30 s, 64 °C for 2 min, 60 °C for 6 min and 72 °C for 30 sec, 72 °C for 2 min with a final authority at 4 °C. Afterwards accumulation the PCR products, amplicons were partially digested with 5 μL of SUPA reagent. Reactions were performed application the afterward conditions: 30 °C for 15 min, 50 °C for 15 min, 55 °C for 15 min, 25 °C for 10 min, 98 °C for 2 min and authority at 4 °C. Libraries were amplified with 4 μL of Ion AmpliSeq HD Dual Barcode Kit with the afterward condition: 99 °C for 15 s, 5 cycles of 99 °C for 15 s, 62 °C for 20 s and 72 °C for 20 s, 15–17 cycles of 99 °C for 15 sec and 70 °C for 40 sec, and 72 °C for 5 min and authority at 4 °C.
There were two mutations empiric in bump samples by Non-MB sequencing, but not by MB sequencing (SMAD4 p. R97H in case #1 and TP53 p.G244S in case #10). For acceptance of these antagonistic results, we amplified the mutations sites with specific primers as follow: 5′-GTGGCTGGTCGGAAAGGATT-3′ and 5′-CCAGGTGATACAACTCGTTCG-3′ for SMAD4 p.R67H; 5′-TGATGATGGTGAGGATGGGC-3′ and 5′-CTGCTTGCCACAGGTCTCC-3′ for TP53 p.G244S. PCR was performed with PrimeSTAR HS DNA Polymerase (TaKaRa Bio, Shiga, Japan). PCR articles were visualized by agarose gel electrophoresis and antiseptic with Agencourt AMPure XP reagents (Beckman Coulter, Brea, CA, USA). End adjustment and barcode adaptors were ligated with Ion Plus Fragment Library Kit in accordance with the manufacturer’s instructions to assemble libraries.
Library ablution was performed application Agencourt AMPure XP reagents (Beckman Coulter) on KingFisher Duo Prime. The library absorption was bent application an Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific); anniversary library was adulterated to 50–60 pM, and the aforementioned bulk of libraries was affiliated for one arrangement reaction. Emulsion PCR and dent loading was performed on the Ion Chef with the Ion 540 Kit-Chef or Ion PI Hi-Q Chef kit; sequencing was performed application Ion 540 Kit-Chef on the Ion GeneStudio S5 Prime Arrangement or Ion PI Hi-Q Sequencing Kit on an Ion Proton Sequencer (Thermo Fisher Scientific).
Sequence abstracts were candy application accepted activity in Torrent Suite Software active on the Torrent Server. Raw arresting abstracts were analyzed application Torrent Suite adaptation 5.10.0. The abstracts processing activity complex signaling processing, abject calling, affection account assignment, adapter trimming, PCR alike removal, apprehend alignment to the animal genome 19 advertence (hg19), affection ascendancy of mapping quality, advantage analysis, and alternative calling. Afterward abstracts analysis, the comment of distinct nucleotide variants, insertions, and deletions was performed by the Ion Reporter Server Arrangement (Thermo Fisher Scientific). Binary SAM (BAM) files were visualized by Ion Reporter Genomic Viewer to assay the alternative in plasma.
For Ion AmpliSeq console assay (Non-MB method), buffy covering DNA was acclimated as a ascendancy to ascertain assured variants in tumors (Tumor–Normal pairs). We acclimated the afterward clarification ambit for alternative calling: (i) the minimum cardinal of alternative allele reads was ≥10, (ii) the advantage abyss was ≥20, (iii) UCSC Common distinct nucleotide polymorphisms (SNPs) = Not In, and (iv) Assured Actual Variants = In.
For Ion AmpliSeq HD console assay (MB method), variants were detected application the workflow of “AmpliSeq HD for Liquid Biopsy w2.1 – DNA – Distinct Sample” with accessory modification. We afflicted ambit in alternative award as follows: (i) minimum cardinal of SNP alternative acknowledging anatomic families = 2, (ii) minimum cardinal of hotspot alternative acknowledging anatomic families = 2, (iii) minimum cardinal of reads with aforementioned different atomic tag (UMT) appropriate to anatomy a anatomic ancestors = 2, (iv) minimum cardinal of admittance and abatement (INDEL) alternative acknowledging anatomic families = 6, and (v) crave ancestors of admeasurement to be anatomic for calling homopolymer INDEL = 2. We acclimated the afterward clarification ambit for alternative calling: (i) Alternate Allele Count ≥2, (ii) UCSC Common SNPs = Not In, (iii) p-value<0.02, (iv) exclude INDEL variants with beneath than VAF < 0.002 or the cardinal of mutated alleles ≤ 3, and (v) exclude non-hotspot variants with the cardinal of mutated alleles ≤3. To ascertain variants in tumors by MB sequencing, the VAF absolute was ≥0.005. Identical mutations agnate to bump DNA were alleged in claret DNA. Arrangement abstracts were visually accepted with the Ion Reporter Genomic Viewer and any sequence, alignment, or alternative alarm absurdity artifacts were discarded. Pathogenic variants were annotated with the OncoKB database38.
If there was a affray in the VAFs amid the MB and non-MB abstracts in the tumour, chiral analysis of the mapping altitude was performed. We empiric two alterations abreast in TP53 gene (c.986 C > G, p.T329S; c.956_978delAGAAGAAACCACTGGATGGAGAA, p.K319fs) in case #8. We visualized BAM files by IGV and aesthetic the mapping altitude (Supplemental Fig. 1A–C). Both two variants exists in the aforementioned sequencing reads. The abstracts possibly showed that FuPa assay removed the album allotment from the best arrangement reads generated by Non-MB, admitting album allotment were charcoal in the reads generated by MB. When Non-MB abstracts was mapped with absence conditions, actual album genitalia would affect the mapping cachet (Supplemental Fig. 1A). Actually, 3′-end of about-face fiber reads from the abatement armpit were not mapped based on alignment scoring condition. The sequencing reads after album allotment independent “soft-clip” arrangement and were not accumbent (Supplemental Fig. 1A). On the added hand, reads with the actual album allotment had a best 3′-end fiber and the absolute arrangement reads with the abatement were aligned. When we adapted the mapping ambit to acquiesce continued insertion/deletion, the VAF added from 26% to 42.6% (Supplemental Fig. 1B). Afore allocation of atomic families based on MB, the raw abstracts of arrangement apprehend showed VAF was 49% (Supplemental Fig. 1C).
All procedures performed in studies involving animal participants were in accordance with the ethical standards of the institutional analytic assay and genome assay board at Yamanashi Central Hospital (G-2018-1) and with the 1964 Helsinki acknowledgment and its after amendments or commensurable ethical standards.
Informed accord was acquired from all alone participants included in the study.
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