This article provides an update on the global cancer burden using the GLOBOCAN 2020 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer. Worldwide, an estimated 19.3 million new cancer cases (18.1 million excluding nonmelanoma skin cancer) and almost 10.0 million cancer deaths (9.9 million excluding nonmelanoma skin cancer) occurred in 2020. Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer, with an estimated 2.3 million new cases (11.7%), followed by lung (11.4%), colorectal (10.0 %), prostate (7.3%), and stomach (5.6%) cancers. Lung cancer remained the leading cause of cancer death, with an estimated 1.8 million deaths (18%), followed by colorectal (9.4%), liver (8.3%), stomach (7.7%), and female breast (6.9%) cancers. Overall incidence was from 2-fold to 3-fold higher in transitioned versus transitioning countries for both sexes, whereas mortality varied <2-fold for men and little for women. Death rates for female breast and cervical cancers, however, were considerably higher in transitioning versus transitioned countries (15.0 vs 12.8 per 100,000 and 12.4 vs 5.2 per 100,000, respectively). The global cancer burden is expected to be 28.4 million cases in 2040, a 47% rise from 2020, with a larger increase in transitioning (64% to 95%) versus transitioned (32% to 56%) countries due to demographic changes, although this may be further exacerbated by increasing risk factors associated with globalization and a growing economy. Efforts to build a sustainable infrastructure for the dissemination of cancer prevention measures and provision of cancer care in transitioning countries is critical for global cancer control.

https://acsjournals.onlinelibrary.wiley.com/doi/pdf/10.3322/caac.21660

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

/pdf/the-genome-analysis-toolkit-a-mapreduce-framework-for-4aygfa9b66.pdf

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.

Availability: http://www.broad.mit.edu/mpg/haploview/

Contact: jcbarret@broad.mit.edu

/pdf/haploview-analysis-and-visualization-of-ld-and-haplotype-1p9iyir38a.pdf

Haploview: analysis and visualization of LD and haplotype maps

Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Availability: Freely available to academic users from: http://www.ub.edu/dnasp

Contact: [email protected]

DnaSP v5

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

https://cdr.lib.unc.edu/downloads/v692t8920

A global reference for human genetic variation.

Recent projects conducted by the International Cancer Genome Consortium (ICGC) have raised the important issue of distinguishing quality assurance (QA) activities from research in the context of genomics. Research was historically defined as a systematic effort to expand a shared body of knowledge, whereas QA was defined as an effort to ascertain whether a specific project met desired standards. However, the two categories increasingly overlap due to advances in bioinformatics and the shift toward open science. As few ethics review policies take these changes into account, it is often difficult to determine the appropriate level of review. Mislabeling can result in unnecessary burdens for the investigators or, conversely, in underestimation of the risks to participants. Therefore, it is important to develop a consistent method of selecting the review process for genomics and bioinformatics projects. This paper begins by discussing two case studies from the ICGC, followed by a literature review on the distinction between QA and research and a comparative analysis of ethics review policies from Canada, the United States, the United Kingdom, and Australia. These results are synthesized into a novel two-step decision tool for researchers and policymakers, which uses traditional criteria to sort clearly defined activities while requiring the use of actual risk levels to decide more complex cases.

/pdf/a-decision-tool-to-guide-the-ethics-review-of-a-challenging-4lnooyddlf.pdf

A decision tool to guide the ethics review of a challenging breed of emerging genomic projects.

The number of population-based and disease-based biobanks being created for research purposes is increasing. These collections of samples and associated data are being used to discover the links between genes and disease, and the genetic, lifestyle and environmental factors behind common complex diseases. In order to make a decision as to whether or not to provide their consent, potential participants in both types of biobanks need to be informed of the requirements and implications of participation. This comparative examination of clauses contained in consent materials from disease biobanks and population biobanks points to the factors that are specific to each type of biobank and highlights the issues that should be taken into consideration when creating consent materials for biobanking activities.

What is in a Clause

Mark A. Rothstein and Bartha Maria Knoppers Many observers have remarked that the law usually lags behind new developments in science and technology, and the following symposium confirms this observation, at least in the context of international genomic research. The legal and policy analyses presented here attempt to reduce the lag time between science and law by calling attention to an emerging trend in genomic research, assessing the current state of the law in 31 representative countries, and proposing a series of recommendations to facilitate genomic research while remaining faithful to the ethical foundations of the laws regulating biomedical research around the world. Research on genetic disorders requires biological specimens (for genome sequencing) and medical records from affected individuals (to confirm the diagnosis, document the symptoms, and track the effect of treatment). Because there are often relatively few cases of a rare disorder, the traditional method of identifying and recruiting potential research participants through a limited number of academic medical institutions has been ineffective. A newer method, using online recruitment — often with the collaboration of patient advocacy and disease-specific groups — has been successful in obtaining greater enrollment. This method has received approval from the IRBs of the researchers’ home institutions. To further increase the number and diversity of participants, some researchers have attempted to use the same recruitment method to enroll participants from other countries. This expansion of scope, however, might be illegal in countries where a researcher from a foreign country may not recruit participants and solicit their biological samples for genomic analysis without ethics approval from the home country of each participant. Because obtaining ethics approval from numerous countries would be infeasible, individuals from many countries are precluded from participating in such studies. Legal restrictions on participation also could delay the research and limit the generalizability of any findings. Consequently, a timely understanding and, if possible, successful resolution of the challenges of international direct-to-participant (DTP) genomic research is essential. Indeed, this issue lies at the intersection of two important and growing trends in biomedical research: internationalization of research and online recruitment of participants.

Regulation of International Direct-to-Participant Genomic Research: Symposium Introduction.

In 2013 Canadian Blood Services (CBS) launched the National Public Cord Blood Bank (NPCBB), a program to collect, process, test, and store cord blood units donated for use in transplantation. A key component of the creation of the NPCBB is the establishment of a program that enables cord blood not suitable for banking or transplantation to be used for biomedical research purposes. Along with the development of processes and policies to manage the NPCBB and the cord blood research program, CBS—in collaboration with researchers from the Stem Cell Network—have also developed educational tools to provide relevant information for target audiences to aid implementation and operation. We describe here one of these tools, the REB Primer on Research and Cord Blood Donation (the Primer), which highlights key ethical and legal considerations and identifies Canadian documents that are relevant to the use of cord blood in biomedical research. The Primer also introduces the NPCBB and describes the systems CBS is implementing to address ethical issues. The Primer is intended to assist research ethics boards in evaluating the ethical acceptability of research protocols, to facilitate harmonized decision-making by providing a common reference, and to highlight the role of research ethics boards in governance frameworks. With the Primer we hope to illustrate how the development of such educational tools can facilitate the ethical implementation and governance of programs related to stem cell research in Canada and abroad.

https://www.jogc.com/article/S1701-2163(15)30260-7/pdf

Bartha Maria Knoppers

Papers

A decision tool to guide the ethics review of a challenging breed of emerging genomic projects.

What is in a Clause

Regulation of International Direct-to-Participant Genomic Research: Symposium Introduction.

Developing Educational Resources to Advance Umbilical Cord Blood Banking and Research: A Canadian Perspective

Biomedical Research Policy