On January 7, 2016, Pacific Biosciences of California, Inc. and BGI announced that BGI has acquired its first Sequel System and plans to purchase additional units in order to further integrate SMRT Sequencing into its global service business.

On February 24, 2016, BGI Genomics launched a genome analytics engine -- BGI Online (beta version) -- using Aliyun cloud computing.

On March 21, 2016, BGI and Think Queensland signed MoU.

On March 25, 2016, BGI announced that it has performed worldwide more than 1 million sequencing-based non-invasive prenatal tests, the NIFTY® test.

On April 20, 2016, BGI Online completed 1000 human whole exome analysis within 22 hours.

On April 25, 2016,Tadataka (Tachi) Yamada, M.D., joins BGI to serve as Chairman of the Scientific Advisory Board (SAB), International Community of Precision Medicine.

On May 11, 2016,BGI and UW Medicine signed a Memorandum of Understanding to collaborate on biomedical technology development.

On May 11, 2016, BGI and Washington State University signed MoU on basic and applied research in agriculture.

On May 16, 2016, BGI signed a partnership agreement with Clearbridge BioMedics.

On May 18, 2016, BGI and the Vancouver Prostate Centre signed MoU.

On June 2, 2016, BGI partnered with Ranomics to classify variants of unknown significance.

On July 20, 2016, an international team of researchers, led by the Centre for Social Evolution in Copenhagen, China National GeneBank and BGI-Shenzhen analyzed the genome sequences of seven farming ant species and their fungus crops. The findings was published today in Nature Communications.

 On August 11, 2016, Dr. Michael C. Dean has been appointed as Advisor of BGI Research. 

On August 15, 2016, BGI announced that it will be offering NRGene's technology as part of its broad genomics analysis services in agriculture research.

On August 16, 2016, BGI opened its new Australian and Asia Pacific headquarters at the QIMR Berghofer Medical Research Institute at Herston, and signed collaboration agreements with leading Queensland researchers: CSIRO, Griffith University and James Cook University.

On September 2, 2016, Shenzhen Precision Medical Research Institute (SZPMRI) was launched today in Shenzhen. BGI, Shenzhen Municipal Health and Family Planning Commission and Shenzhen Municipal Public Hospital Administration Center will work together to promote the development of precision medical research and clinical application.

On September 22, 2016, the China National GeneBank (CNGB) officially opened.
On October 21, 2016, BGI and QIMR Berghofer Medical Research Institute have entered into an agreement that will promote collaboration on a genomics-based research and education program.
BGI formed a global partnership with five leading health and research organizations (Providence Health Care,On October 22, 2016, St. Paul’s Foundation, Vancouver Prostate Centre (VPC), Genome British Columbia (Genome BC), and Deloitte Inc.) in British Columbia to bring together advanced technologies and individualized therapy for cancer and other diseases.
On October 28, 2016, GigaScience joins the Oxford University Press journals program
On October 31, 2016, BGI announced that it joins the International Gene Synthesis Consortium (IGSC).
On November 1, 2016, BGI and metaSysX GmbH sign a joint agreement on life science and healthcare

On November 5, 2016, BGI Launches the Latest Desktop Sequencer BGISEQ-50.
From November 4 to November 6, 2016, The 11th International Conference on Genomics (ICG-11) was successfully held in the China National Genebank.

On November 17, 2016, Prof. Huanming Yang, the co-founder and Chairman of BGI-China, was awarded as the foreign member of Royal Danish Academy of Sciences and Letters.
On November 22, 2016, GigaScience published an article that presents the genome sequence of Ginkgo biloba, the oldest extant tree species. The research was carried out by a team of scientists at BGI, Zheijiang University and the Chinese Academy of Sciences, who tackled and analyzed an exceptionally large genome, totalling more than 10 billion DNA “letters”.
On December 15, 2016, BGI involved in publication of the first seahorse genome in Nature.