Hepatocellular carcinoma (HCC) is one of the most common solid tumors worldwide, and is particularly prevalent in Asia, being the third most common cause of cancer-related death. Hepatitis B virus (HBV) is a major etiologic agent, leading to an increased risk of developing HCC, in particular those with acute liver disease and cirrhosis. The Asian Cancer Research Group (ACRG) is an independent, not-for-profit company established to accelerate research and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Bringing together pharmaceutical partners from Eli Lily, Merck, and Pfizer, with academic partners at Hong Kong University, National University of Singapore and BGI, with the aim to create one of the most extensive open pharmacogenomic cancer datasets known to date. With HBV being endemic in China and Southeast Asia, and high levels of HCC being a result, the ACRG have studied the events and effects of HBV integration in the HCC genome. To do this massively parallel sequencing in a cohort of 88 Chinese patients diagnosed with HCC who underwent curative primary hepatectomy or liver transplantation at Queen Mary Hospital (Pokfulam, Hong Kong) was carried out. Of these 81 were HBV-positive and 7 HBV-negative. All patients gave written informed consent to use both tumour (T) and non-tumour (N) liver tissues for the study and open sharing of the data. Genomic DNA was purified for at least 30-fold coverage paired-end (PE) sequencing, and PE reads were mapped on human reference genome (UCSC build hg19) and HBV (NC_003977). Two sequencing libraries with different insert size were constructed for each genomic DNA sample (200 bp and 800 bp). Paired end, 90bp read length sequencing was performed in the HiSeq 2000 sequencer according to Manufacturer’s instructions.
The results of this are published in Nature Genetics: doi: 10.1038/ng.2295.
Included here for access is data from Hong Kong’s first emblematic genome project: BauhiniaGenome. Hong Kong’s emblem is the beautiful Bauhinia blakeana flower and appears on our flag and currency. What many people may not know is that it is a sterile hybrid, and how and why it ended up in Hong Kong is shrouded in mystery.
By bringing together the emblematic and mysterious Bauhinia flower and the power and knowledge of genome technology, we can build a bridge between science and community— enlightening our understanding of this plant’s interesting biology and informing and educating the public about this exciting and rapidly advancing field.
To build such a collaborative endeavor, we have launched the first Hong Kong genome project through which we will sequence the genome of the Hong Kong emblem to better understand where it came from; train local students to assemble and analyse the data — crucial skills needed for this field to advance; and engage the public through local pride.
The data presented here are four transcriptome datasets: leaf and flower data from Bauhinia blakeana as well as leaf transcriptomes from the most likely parent species Bauhinia purpurea and Bauhinia variegata. Specimens were collected in Hong Kong, and sequenced at the laboratories of BGI Hong Kong using the Illumina HiSeq 4000 platform. RNA was extracted using protocols available at protocols.io (see: dx.doi.org/10.17504/protocols.io.gsnbwde). These data are made available here for analysis and the open-source teaching of transcriptomics analysis.