Informatics for Next-Generation Sequencing

Our new book Next-Generation DNA Sequencing Informatics is the first of its kind to address the informatics needs of scientists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies.

Edited by Stuart Brown, the book includes contributions from researchers at New York University’s Langone Medical Center, which invested heavily and early in next-generation sequencing (NGS) technology and informatics capacity. “In this book, building on our own extensive experience that spans collaborations on more than 30 National Institutes of Health-funded projects, and by critically evaluating and synthesizing the literature in the field, we provide an overview of many core types of next-generation sequencing projects, a discussion of methods embodied in popular software, and detailed descriptions of our own best practice workflows,” writes Brown.

 Topics include data visualization, sequence alignment, genome assembly and annotation, variant discovery, RNA-seq, ChIP-seq, and metagenomics, as well as the history of DNA sequencing and informatics. An accompanying website, seqinformatics.com, offers tutorials and resources for NGS. For additional details on the book, click here.

 

Archived Guthrie cards find a new purpose

A newborn’s blood spotted onto a Guthrie card. Photo: The New York State Department of Health Newborn Screening Program.

Over the last 50 years, the spotting of newborn’s blood onto filter paper for disease screening, called Guthrie cards, has become so routine that since 2000, more than 90% of newborns in the United States have had Guthrie cards created.  In a study published online in Genome Research (www.genome.org), researchers have shown that epigenetic information stored on archived Guthrie cards provides a retrospective view of the epigenome at birth, a powerful new application for the card that could help understand disease and predict future health.

DNA methylation, an epigenetic chemical modification of DNA, is known to affect gene activity and play a role in normal development, aging, and also in diseases such as heart disease, diabetes, and cancer.  “But are these epigenetic marks involved in causing the disease, or a result of the disease itself?” asked Dr. Vardhman Rakyan of Queen Mary, University of London and co-senior author of the study.  Rakyan explained that this is impossible to know when samples are obtained after onset of the disease.  Guthrie cards, commonly used to collect blood spots from the pricked heel of newborns to screen for diseases such as phenylketonuria, cystic fibrosis, and sickle cells disorders, might offer a snapshot of the epigenome before disease develops.  Many Guthrie cards are stored indefinitely by health authorities around the world, posing a potential wealth of information about the epigenome at birth.

Rakyan and an international group of colleagues purified genomic DNA and analyzed DNA methylomes from Guthrie cards and verified that this archived DNA yields high-quality methylation data when compared to fresh samples.  The researchers then compared the DNA methylation profiles of newborns to the same healthy individuals at the age of three, looking for epigenetic variations detected in the Guthrie card sample that are stable into the early years of life.

“We found similar epigenetic differences between different people both at birth and when they were three years old,” said Rakyan, who added that these differences, already present at birth, are unlikely due solely to inherent genetic differences between the individuals, but also due to environment or random events in utero.  Furthermore, Guthrie card samples could be analyzed for both genetic and epigenetic differences together to view a more complete picture of the genome at birth.

Guthrie card methylomics is a potentially powerful new application for archived blood spots, which could provide a wealth of information about epigenetics and disease, and could give clues about health later in life.  Dr. David Leslie, co-senior author of the study, added that because national health authorities routinely make Guthrie cards available, and with the proper consent obtained from parents and children, “we are talking about an invaluable, and non-renewable, resource for millions of individuals.”

 

Differences between human twins at birth highlight importance of intrauterine environment

Your genes determine much about you, but environment can have a strong influence on your genes even before birth, with consequences that can last a lifetime.  In a study published online in Genome Research (www.genome.org), researchers have for the first time shown that the environment experienced in the womb defines the newborn epigenetic profile, the chemical modifications to DNA we are born with, that could have implications for disease risk later in life.

Epigenetic tagging of genes by a chemical modification called DNA methylation is known to affect gene activity, playing a role in normal development, aging, and also in diseases such as diabetes, heart disease, and cancer.  Studies conducted in animals have shown that the environment shapes the epigenetic profile across the genome, called the epigenome, particularly in the womb.  An understanding of how the intrauterine environment molds the human epigenome could provide critical information about disease risk to help manage health throughout life.

Twin pairs, both monozygotic (identical) and dizygotic (fraternal), are ideal for epigenetic study because they share the same mother but have their own umbilical cord and amniotic sac, and in the case of identical twins, also share the same genetic make-up.  Previous studies have shown that methylation can vary significantly at a single gene across multiple tissues of identical twins, but it is important to know what the DNA methylation landscape looks like across the genome.

In this report, an international team of researchers has for the first time analyzed genome-scale DNA methylation profiles of umbilical cord tissue, cord blood, and placenta of newborn identical and fraternal twin pairs to estimate how genes, the shared environment that their mother provides and the potentially different intrauterine environments experienced by each twin contribute to the epigenome.  The group found that even in identical twins, there are widespread differences in the epigenetic profile of twins at birth.

“This must be due to events that happened to one twin and not the other,” said Dr. Jeffrey Craig of the Murdoch Childrens Research Institute (MCRI) in Australia and a senior author of the report.  Craig added that although twins share a womb, the influence of specific tissues like the placenta and umbilical cord can be different for each fetus, and likely affects the epigenetic profile.

Interestingly, the team found that methylated genes closely associated with birth weight in their cohort are genes known to play roles in growth, metabolism, and cardiovascular disease, lending further support to a known link between low birth weight and risk for diseases such as diabetes and heart disease.  The authors explained that their findings suggest the unique environmental experiences in the womb may have a more profound effect on epigenetic factors that influence health throughout life than previously thought.

Furthermore, an understanding of the epigenetic profile at birth could be a particularly powerful tool for managing future health.  “This has potential to identify and track disease risk early in life, said Dr. Richard Saffery of the MCRI and a co-senior author of the study, “or even to modify risk through specific environmental or dietary interventions.”

 

Gut microbes battle a common set of viruses shared by global populations

The human gut is home to a teeming ecosystem of microbes that is intimately involved in both human health and disease.  But while the gut microbiota is interacting with our body, they are also under constant attack from viruses.  In a study published online in Genome Research, researchers have analyzed a bacterial immune system, revealing a common set of viruses associated with gut microbiota in global populations.

Viruses that prey on bacteria, called phages, pose a constant threat to the health of bacterial communities.  In many ecological systems, viruses outnumber bacterial cells ten to one.  Given the richness of bacteria in the human gut, it was not surprising that scientists have found that phages are also highly prevalent.  But how can viruses targeting gut microbiota be identified?  How do viral communities differ between people and global populations, and what could this tell us about human health and disease?

In this report, a team of scientists from Israel has taken advantage of information coded in a bacterial immune system to shed new light on these questions.  Bacteria can “steal” small pieces of DNA from phages that attack them, and use these stolen pieces to recognize and respond to the attacker, in a manner similar to usage of antibodies by the human immune system. The stolen DNA pieces are stored in specific places in the bacterial genome called CRISPR loci (clustered regularly interspaced short palindromic repeats).

“In our study we searched for such stolen phage DNA pieces carried by bacteria living in the human gut,” said Rotem Sorek of the Weizmann Institute of Science and senior author of the study.  “We then used these pieces to identify DNA of phages that co-exist with the bacteria in the gut.”

Sorek’s team used this strategy to identify and analyze phages present in the gut microbiota of a cohort of European individuals.  They found that nearly 80% of the phages are shared between two or more individuals.  The team compared their data to samples previously derived from American and Japanese individuals, finding phages from their European data set also present in these geographically distant populations, a surprising result given the diversity of phages seen in other ecological niches.

Sorek explained that their findings mean that there are hundreds of types of viruses that repeatedly infect our gut microbiota.  “These viruses can kill some of our gut bacteria,” said Sorek. “It is therefore likely that these viruses can influence human health.”

The authors note that as evidence for the beneficial roles played by bacteria in the healthy human gut continues to mount, it is critical that we understand the pressures placed upon the “good” bacteria that are vital to human health.  “Our discovery of a large set of phages attacking these good bacteria in our gut opens a window for understanding how they affect human health,” Sorek added.  Researchers can now begin to ask how phage dynamics in the gut changes over time, and what it might tell us about diseases, such as inflammatory bowel disease, and how to more effectively treat them.

 

The Biology of the Human Genome

There’s much excitement here at CSHL in anticipation of the popular annual Biology of Genomes meeting, which begins tonight. For the next 6 days, scientists from around the world will assemble on campus to discuss the latest advances in genome research as they relate to evolution, biology, and disease in a variety of organisms—including humans.

This year marks the 10^th anniversary of the publication of the draft human genome sequence. What has it told us about human biology? Do we know the function of every gene in the human genome?

To address these questions, Stewart Scherer has spent substantial time and effort compiling information from the scientific literature about human genes and their biological functions.  The result is a new online resource, Guide to the Human Genome, that puts the genes of the human genome in their biological context. The Guide, available at www.humangenomeguide.org, provides extensive up-to-date information about human genes in an easily accessible format.