Sureselect probes

Manufactured by Agilent Technologies

SureSelect probes are DNA/RNA capture probes designed for targeted sequencing applications. They are used to selectively enrich and capture regions of interest from a sample prior to sequencing.

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Lab products found in correlation

Hiseq 2000, by Illumina (2 mentions) Clc bio, by Qiagen (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Truseq dna sample preparation kit, by Illumina (1 mentions)

4 protocols using sureselect probes

Massively Parallel Sequencing of 9p21 Region

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Since some of the variants found in this study were not standardized and clinically validated mutations, we used massively parallel sequencing of hybrid-captured DNA to further evaluate preliminary findings from MLPA screening of genes in the 9p21 region. Agilent SureSelect probes were designed to capture the genomic regions of CDKN2A and CDKN2B, including introns and 20 kb adjacent 5′ and 3′ regions, which covered the regions implicated by MLPA. Paired-end sequencing 2 × 100 bp was performed on the Illumina HiSeq2000 instrument to an average depth of >100 reads, followed by alignment to the reference genome. Coverage over the suspected deleted/duplicated regions was not found to be different from coverage in control samples.

Andersson U., Wibom C., Cederquist K., Aradottir S., Borg Å., Armstrong G.N., Shete S., Lau C.C., Bainbridge M.N., Claus E.B., Barnholtz-Sloan J., Lai R., Il'yasova D., Houlston R.S., Schildkraut J., Bernstein J.L., Olson S.H., Jenkins R.B., Lachance D.H., Wrensch M., Davis F.G., Merrell R., Johansen C., Sadetzki S., Bondy M.L., Melin B.S., Adatto P., Morice F., Payen S., McQuinn L., McGaha R., Guerra S., Paith L., Roth K., Zeng D., Zhang H., Yung A., Aldape K., Gilbert M., Weinberger J., Colman H., Conrad C., de Groot J., Forman A., Groves M., Levin V., Loghin M., Puduvalli V., Sawaya R., Heimberger A., Lang F., Levine N., Tolentino L., Saunders K., Thach T.T., Iacono D.D., Sloan A., Gerson S., Selman W., Bambakidis N., Hart D., Miller J., Hoffer A., Cohen M., Rogers L., Nock C.J., Wolinsky Y., Devine K., Fulop J., Barrett W., Shimmel K., Ostrom Q., Barnett G., Rosenfeld S., Vogelbaum M., Weil R., Ahluwalia M., Peereboom D., Staugaitis S., Schilero C., Brewer C., Smolenski K., McGraw M., Naska T., Rosenfeld S., Ram Z., Blumenthal D.T., Bokstein F., Umansky F., Zaaroor M., Cohen A., Tzuk-Shina T., Voldby B., Laursen R., Andersen C., Brennum J., Henriksen M.B., Marzouk M., Davis M.E., Boland E., Smith M., Eze O., Way M., Lada P., Miedzianowski N., Frechette M., Paleologos N., Byström G., Svedberg E., Huggert S., Kimdal M., Sandström M., Brännström N., Hayat A., Tihan T., Zheng S., Berger M., Butowski N., Chang S., Clarke J., Prados M., Rice T., Sison J., Kivett V., Duo X., Hansen H., Hsuang G., Lamela R., Ramos C., Patoka J., Wagenman K., Zhou M., Klein A., McGee N., Pfefferle J., Wilson C., Morris P., Hughes M., Britt-Williams M., Foft J., Madsen J., Polony C., McCarthy B., Zahora C., Villano J., Engelhard H., Borg A., Chanock S.K., Collins P., Elston R., Kleihues P., Kruchko C., Petersen G., Plon S., Thompson P., Johansen C., Sadetzki S., Melin B., Bondy M.L., Lau C.C., Scheurer M.E., Armstrong G.N., Liu Y., Shete S., Yu R.K., Aldape K.D., Gilbert M.R., Weinberg J., Houlston R.S., Hosking F.J., Robertson L., Papaemmanuil E., Claus E.B., Claus E.B., Barnholtz-Sloan J., Sloan A.E., Barnett G., Devine K., Wolinsky Y., Lai R., McKean-Cowdin R., Il'yasova D., Schildkraut J., Sadetzki S., Yechezkel G.H., Bruchim R.B., Aslanov L., Sadetzki S., Johansen C., Kosteljanetz M., Broholm H., Bernstein J.L., Olson S.H., Schubert E., DeAngelis L., Jenkins R.B., Yang P., Rynearson A., Andersson U., Wibom C., Henriksson R., Melin B.S., Cederquist K., Aradottir S., Borg Å., Merrell R., Lada P., Wrensch M., Wiencke J., Wiemels J., McCoy L., McCarthy B.J, & Davis F.G. (2014). Germline rearrangements in families with strong family history of glioma and malignant melanoma, colon, and breast cancer. Neuro-Oncology, 16(10), 1333-1340.

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Targeted NGS Analysis of APC Gene

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Targeted NGS was performed on a genomic DNA sample extracted from whole blood from the proband in the Genomics Laboratory at Mayo Clinic (Test code: APCZ). Briefly, genomic DNA was sheared by sonication and captured using SureSelect probes (Agilent). Then, paired-end sequencing (2 × 101 bp) was performed on Illumina HiSeq 2500 platform (Illumina). NGS data were analyzed using CLC Bio (QIAGEN) and in-house-developed bioinformatic tools. APC coding exons and flanking noncoding region (transcript NM_ 000038) were analyzed with average coverage at ∼4000× in this sample. The reportable variant was verified by Sanger sequencing. Targeted Sanger sequencing analyses were performed on parental samples received (Test code: FMTT). (See Table 2.)

Kiessling P., Dowling E., Huang Y., Ho M.L., Balakrishnan K., Weigel B.J., Highsmith WE J.r., Niu Z, & Schimmenti L.A. (2019). Identification of aggressive Gardner syndrome phenotype associated with a de novo APC variant, c.4666dup. Cold Spring Harbor Molecular Case Studies, 5(2), a003640.

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Illumina Sequencing Library Prep

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We used the Illumina TruSeq DNA Sample Preparation Kit (Illumina, CA, USA) with 12 multiplexed adapters. Multiplexed DNA libraries were pooled at equal molar ratio before hybridization with the custom Agilent Sure Select probes. Following elution of captured sequence, we performed 6–8 cycles of PCR-based amplification. Samples passing standard quality-control (QC) metrics were sequenced on the Illumina HiSeq2000 (Illumina, CA, USA). Twelve multiplexed samples were sequenced per lane using 75 base pair-end read module.

Pirooznia M., Wang T., Avramopoulos D., Potash J., Zandi P, & Goes F. (2015). High-throughput sequencing of the synaptome in major depressive disorder. Molecular psychiatry, 21(5), 650-655.

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Capture Hi-C Profiling of ZIP13K2

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cHi-C libraries were prepared from CRISPRi sgCtrl or sgT-REX17 EN cells. 5x10⁶ ZIP13K2-derived EN cells were harvested and washed with ice cold DPBS. Cell lysis, NlaIII (NEB, R0125) digestion and proximity-ligation was performed according to the Franke et al. protocol (Franke et al., 2016 (link)) with minor changes. Adaptors were added to DNA fragments and amplified according to Agilent Technologies instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect probes (Agilent Technologies, 5190–4806/3253271) (s. probe list in Supplementary file 3) and indexed for sequencing of 200 M fragments /sample (100 bp paired-end) following the Agilent instructions. Capture Hi-C experiments were performed as biological duplicates.

Landshammer A., Bolondi A., Kretzmer H., Much C., Buschow R., Rose A., Wu H.J., Mackowiak S.D., Braendl B., Giesselmann P., Tornisiello R., Parsi K.M., Huey J., Mielke T., Meierhofer D., Maehr R., Hnisz D., Michor F., Rinn J.L, & Meissner A. (2023). T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife, 12, e83077.

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