Saphyr g2.3 chip

Manufactured by Bionano Genomics

The Saphyr G2.3 chip is a key component of the Saphyr System, a platform developed by Bionano Genomics for optical genome mapping. The chip is designed to facilitate the analysis of high-molecular-weight DNA molecules using the Saphyr System's proprietary technology.

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Lab products found in correlation

Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Saphyr instrument, by Bionano Genomics (2 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Sp blood and cell culture dna isolation kit, by Bionano Genomics (2 mentions) Qubittm dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Qubittm dsdna br assay kit, by Thermo Fisher Scientific (1 mentions) Dls dna labeling kit, by Bionano Genomics (1 mentions) Sp blood cell culture dna isolation kit, by Bionano Genomics (1 mentions) Prep direct label and stain dls protocol, by Bionano Genomics (1 mentions) Phenylmethylsulfonyl fluoride pmsf, by Merck Group (1 mentions) Solve v 3, by Bionano Genomics (1 mentions) Dls labeling kit, by Bionano Genomics (1 mentions)

5 protocols using saphyr g2.3 chip

Optical Genome Mapping of Cell Samples

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Optical Genome Mapping (OGM) was performed according to the manufacturer’s instructions. Briefly, DNA was isolated from 1.5 × 10⁶ frozen cells using the Bionano Prep SP Frozen Cell Pellet DNA Isolation Protocol v2 (#30398 Rev B, Bionano Genomics Inc., San Diego, CA, USA). The DNA concentration was determined with the Qubit^TM dsDNA BR Assay Kit and a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). Subsequently, the DNA was labeled with Bionano Prep Direct Label and Stain Kit (Protocol #30206 Rev G; Bionano Genomics Inc.) and the concentration determined with the Qubit^TM dsDNA HS Assay Kit and a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). The labeled DNA was loaded on a Saphyr G2.3 chip and imaged with the Saphyr device (Bionano Genomics Inc.). The data were analyzed and visualized on the Bionano Access Server with the de novo pipeline (Tools Version 1.7.1, reference genome GRCh38/hg38). The recommended filter settings were applied and the frequency of SVs in the Bionano control database was set to 0%.

Nowak J., Bentele M., Kutle I., Zimmermann K., Lühmann J.L., Steinemann D., Kloess S., Koehl U., Roßberg W., Ahmed A., Schaudien D., Neubert L., Kamp J.C., Kuehnel M.P., Warnecke A., Schambach A, & Morgan M. (2023). CAR-NK Cells Targeting HER1 (EGFR) Show Efficient Anti-Tumor Activity against Head and Neck Squamous Cell Carcinoma (HNSCC). Cancers, 15(12), 3169.

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Fluorescent Labeling of UHMW gDNA

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The isolated UHMW gDNA was fluorescently labeled using the Bionano Prep DNA Labeling Kit-DLS (Bionano Genomics, 80005) according to the Prep Direct Label and Stain (DLS) Protocol (Bionano Genomics). In short, Direct Label Enzyme (DLE-1) and DL-green fluorophores were used to label 750 ng of purified gDNA at a specific sequence motif. After a cleanup of the fluorophores excess, DNA backbone was counterstained overnight before quantitation with Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32851). Finally, the labeled UHMW gDNA molecules were loaded on a Saphyr G2.3 chip for sequentially imaging across nanochannels on the Saphyr instrument (Bionano Genomics).

Pongor L.S., Schultz C.W., Rinaldi L., Wangsa D., Redon C.E., Takahashi N., Fialkoff G., Desai P., Zhang Y., Burkett S., Hermoni N., Vilk N., Gutin J., Rona G., Zhao Y., Nichols S., Vilimas R., Sciuto L., Graham C., Caravaca J.M., Turan S., Shen T.W., Rajapakse V.N., Kumar R., Upadhyay D., Kumar S., Kim Y.S., Roper N., Tran B., Hewitt S.M., Kleiner D.E., Aladjem M.I., Friedman N., Hager G.L., Pommier Y., Ried T, & Thomas A. (2023). Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and is Associated with Worse Outcomes. Cancer discovery, 13(4), 928-949.

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Optical Genome Mapping for Tumor Analysis

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We extracted high-molecular-weight (HMW) DNA from PBMNC or BMMNC at initial diagnosis using the SP Blood and Cell Culture DNA Isolation Kit, according to the manufacturer’s guidelines (Bionano Genomics, San Diego, CA). In addition, HMW DNA was extracted from remission material or fibroblasts (if available) of the respective children as matching nontumor control. Labeling of HMW DNA was performed using the DLS DNA Labeling Kit (Bionano Genomics), according to the manufacturer’s protocol (Bionano Prep Direct Label and Stain [DLS] Protocol 30206). The labeled DNA was loaded on a Saphyr G2.3 chip and molecules were imaged using the Saphyr instrument (Gen 2, Bionano Genomics). Overall, we performed OGM on 60 matched tumor/non-tumor pairs (120 samples), and 1 sequential sample including tumor material from initial diagnosis and relapse in comparison to matched non-tumor material (ALL4). Refer to Suppl. Figure S2 for an overview of the applied OGM workflow.

Brandes D., Yasin L., Nebral K., Ebler J., Schinnerl D., Picard D., Bergmann A.K., Alam J., Köhrer S., Haas O.A., Attarbaschi A., Marschall T., Stanulla M., Borkhardt A., Brozou T., Fischer U, & Wagener R. (2023). Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia. HemaSphere, 7(8), e925.

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Optical Genome Mapping for Rare Variant Detection

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OGM was performed as previously described [33 (link), 34 (link)]. In brief, high‐molecular‐weight germline DNA was extracted from an Epstein–Barr virus (EBV)‐transformed lymphoblastoid cell line from II‐2, using the SP Blood & Cell Culture DNA Isolation Kit according to the manufacturer's instructions (Bionano Genomics®, San Diego, CA, USA). The cell pellet (1.5 million cells) was resuspended in proteinase K and RNAse and mixed with LBB‐lysis buffer to release genomic DNA (gDNA). The sample was treated with phenyl‐methyl‐sulfonyl‐fluoride (PMSF) (Sigma‐Aldrich, St Louis, MO, USA), and isopropanol was added after placing a Nanobind disk on each sample. After washing, gDNA was eluted from the disks and equilibrated overnight to facilitate DNA homogeneity. Next, gDNA was labeled according to the manufacturer's instructions using the Bionano Prep Direct Label and Stain (DLS) Protocol. The sample was subsequently stained overnight using the Bionano DNA stain reagent and loaded on a 3 × 1300 Gb Saphyr chip (G2.3) to be imaged using the Saphyr instrument. Bionano Solve v3.4 was used to perform the de novo genome assembly, variant calling, and annotation with default settings. Annotated variants were filtered for rare events as described previously [34 (link)].

Sabatella M., Mantere T., Waanders E., Neveling K., Mensenkamp A.R., van Dijk F., Hehir‐Kwa J.Y., Derks R., Kwint M., O'Gorman L., Tropa Martins M., Gidding C.E., Lequin M.H., Küsters B., Wesseling P., Nelen M., Biegel J.A., Hoischen A., Jongmans M.C, & Kuiper R.P. (2021). Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. The Journal of Pathology, 255(2), 202-211.

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Optical Genome Mapping of Biallelic SVs

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OGM was performed for patient 1, harboring biallelic SVs. Ultra-high molecular weight DNA was extracted from 1.5 million lymphoblastoid cells using the SP Blood and Cell Culture DNA Isolation Kit according to the manufacturer’s instructions (Bionano Genomics) (Mantere et al, 2021 (link); Bruijn et al, 2022 (link)). DNA was labeled using a DLS Labeling Kit (Bionano Genomics). The labeled DNA was loaded on a Saphyr chip G2.3 and run on a Saphyr instrument (Bionano Genomics) for an output of 400 Gb. De novo assembly and variant annotation of the OGM data were conducted on Bionano Solve software version 3.7. We focused on FGF12 and visualized it on Bionano Access 1.7.1.1.

Ohori S., Miyauchi A., Osaka H., Lourenco C.M., Arakaki N., Sengoku T., Ogata K., Honjo R.S., Kim C.A., Mitsuhashi S., Frith M.C., Seyama R., Tsuchida N., Uchiyama Y., Koshimizu E., Hamanaka K., Misawa K., Miyatake S., Mizuguchi T., Saito K., Fujita A, & Matsumoto N. (2023). Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy. Life Science Alliance, 6(8), e202302025.

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