Genomic landscape and PD-1 blockade in Natural-killer/T cell lymphoma

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Dataset ID	Description	Technology	Samples
EGAD00001003271	WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded.	Illumina HiSeq 2000	102
EGAD00001004140	Whole-genome sequencing (WGS) was performed for 13 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively. 8 NKTL FFPE specimens were screened for somatic mutations using deep targeted capture sequencing (TCS). FFPE rolls or slides were extracted using QIAamp DNA FFPE Tissue kit (QIAGEN). The FFPE genomic DNA was treated with NEBNext FFPE DNA Repair Mix and assessed by Quant-it PicoGreen dsDNA Assay Kit (Invitrogen). The library was generated from 10-200 ng DNA with SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent Technologies) according to manufacturer’s instructions. RNA based probe was designed with SureDesign (Agilent Technologies) to target-capture 140 genes. Next, the captured libraries were pooled in equimolar concentration and sequenced on Illumina Novaseq 6000 platform with SP or S1 chip. Reads aligning to 40 selected genes were isolated post-alignment for this submission. Prefix used in filenames: T - Tumor samples N - Matched-Normal samples	HiSeq X Ten Illumina HiSeq 2000 Illumina NovaSeq 6000	34
EGAD00001005230	Whole-transcriptome sequencing (WTS) of 36 samples from patients diagnosed with NKTL. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.	HiSeq X Ten Illumina HiSeq 2000 Illumina HiSeq 2500	36
EGAD00001005231	Whole-genome sequencing (WGS) was performed for 50 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000 or HiSeq X Ten as 2x101 bp or 2x151 bp, respectively.	HiSeq X Ten Illumina HiSeq 2000	120
EGAD00001005303	211 NKTL FFPE specimens were screened for somatic mutations using deep targeted capture sequencing. FFPE rolls or slides were extracted using QIAamp DNA FFPE Tissue kit (QIAGEN). The FFPE genomic DNA was treated with NEBNext FFPE DNA Repair Mix and assessed by Quant-it PicoGreen dsDNA Assay Kit (Invitrogen). The library was generated from 10-200 ng DNA with SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent Technologies) according to manufacturer’s instructions. RNA based probe was designed with SureDesign (Agilent Technologies) to target-capture 140 genes. Next, the captured libraries were pooled in equimolar concentration and sequenced on Illumina Novaseq 6000 platform with SP or S1 chip.	Illumina NovaSeq 6000	214

Publications	Citations
Whole-genome sequencing identifies responders to Pembrolizumab in relapse/refractory natural-killer/T cell lymphoma. Lim JQ, Huang D, Tang T, Tan D, Laurensia Y, Peng RJ, Wong EKY, Cheah DMZ, Chia BKH, Iqbal J, Grigoropoulos NF, Nairismägi ML, Ng CCY, Rajasegaran V, Hong H, Kim SJ, Cho J, Tse E, Mow B, Cai QC, Poon LM, Cai QQ, Tan J, Chan JY, Lim JX, Goh YT, Phipps C, Rötzschke O, Cheng CL, Ha JCH, Khoo LP, Loh YSM, Au-Yeung R, Chan TS, Kwong YL, Hwang W, Kim WS, Bei JX, Lin T, Ong CK, Lim ST. Leukemia 34: 2020 3413-3419	38
Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression. Chen Z, Huang H, Hong H, Huang H, Weng H, Yu L, Xiao J, Wang Z, Fang X, Yao Y, Yue JX, Lin T. Genome Med 16: 2024 48	0

Publications

Citations

Whole-genome sequencing identifies responders to Pembrolizumab in relapse/refractory natural-killer/T cell lymphoma.
Lim JQ, Huang D, Tang T, Tan D, Laurensia Y, Peng RJ, Wong EKY, Cheah DMZ, Chia BKH, Iqbal J, Grigoropoulos NF, Nairismägi ML, Ng CCY, Rajasegaran V, Hong H, Kim SJ, Cho J, Tse E, Mow B, Cai QC, Poon LM, Cai QQ, Tan J, Chan JY, Lim JX, Goh YT, Phipps C, Rötzschke O, Cheng CL, Ha JCH, Khoo LP, Loh YSM, Au-Yeung R, Chan TS, Kwong YL, Hwang W, Kim WS, Bei JX, Lin T, Ong CK, Lim ST. Leukemia 34: 2020 3413-3419

Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression.
Chen Z, Huang H, Hong H, Huang H, Weng H, Yu L, Xiao J, Wang Z, Fang X, Yao Y, Yue JX, Lin T. Genome Med 16: 2024 48