Distinguishing amplification artifacts from biologically derived somatic mutations in single-cell sequencing data

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

Craig L. Bohrson, Alison R. Barton, Michael A. Lodato, Rachel E. Rodin, Lovelace J. Luquette, Vinay V. Viswanadham, Doga C. Gulhan, Isidro Cortés-Ciriano, Maxwell A. Sherman, Minseok Kwon,  Michael E. Coulter, Alon Galor, Christopher A. Walsh & Peter J. Park

Nature Genetics (Research Article)

Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of mutational heterogeneity in normal and diseased tissues. However, a major difficulty is distinguishing amplification artifacts from biologically derived somatic mutations. Here, we describe linked-read analysis (LiRA), a method that accurately identifies somatic single-nucleotide variants (sSNVs) by using read-level phasing with nearby germline heterozygous polymorphisms, thereby enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells.

Google AI variant caller goes deep on rice genomes

Analyzing 3024 rice genomes characterized by DeepVariant

“Rice is an ideal candidate for study in genomics, not only because it’s one of the world’s most important food crops, but also because centuries of agricultural cross-breeding have created unique, geographically-induced differences. With the potential for global population growth and climate change to impact crop yields, the study of this genome has important social considerations.

This post explores how to identify and analyze different rice genome mutations with a tool called DeepVariant. To do this, we performed a re-analysis of the Rice 3Kdataset and have made the data publicly available as part of the Google Cloud Public Dataset Program pre-publication and under the terms of the Toronto Statement.

We aim to show how AI can improve food security by accelerating genetic enhancement to increase rice crop yield. According to the Food and Agriculture Organization of the United Nations, crop improvements will reduce the negative impact of climate change and loss of arable land on rice yields, as well as support an estimated 25% increase in rice demand by 2030.”

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Standardized Germline Variant Calling Performance Metrics

GA4GH Benchmarking Team Releases Best Practices for Comparing Germline Variant Calls

NEW YORK (GenomeWeb) – Members of the benchmarking team of the Global Alliance for Genomics and Health have developed methods for producing standardized performance metrics for benchmarking small germline variant calls.

The GA4GH Benchmarking team brings together participants from research institutes, technology companies, government agencies, and clinical laboratories. It includes researchers from the National Institute of Standards and Technology (NIST), Illumina, Ontario Institute for Cancer Research, DNAnexus, and others.

As explained in a Nature Biotechnology paper published yesterday, the methods that they have developed address challenges associated with standardizing metrics like recall and precision, comparing different representations of variant calls, and stratifying performance by variant type and genome context. The team has made the code used for the benchmarking available in Github.

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Personalis introduces new universal cancer immunogenomics platform, ImmunoID NeXT™

Personalis, Inc. to Present at ICI-IO Combinations Summit 2019

MENLO PARK, Calif.--(BUSINESS WIRE)--Personalis Inc., a leader in advanced genomics for precision oncology, today announced that they are scheduled to present at ICI-IO Combinations Summit 2019 in Boston on Wednesday, March 20, 2019 at 2:30 PM, EDT.

The presentation, entitled “Challenges and Solutions: Enabling multidimensional tumor immunogenomics for advancing biomarker discovery,” will introduce Personalis’ new universal cancer immunogenomics platform, ImmunoID NeXT™. In addition to an overview, the presentation will also highlight how this platform can be used to overcome the challenges facing immuno-oncology translational and clinical researchers. By deriving new insights through our industry leading NGS analysis platform, ImmunoID NeXT provides solutions to enable the development of safer, more effective precision oncology therapeutics and combinations.

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Improve clinical care for Ovarian cancer using multiple genome sequences

Simultaneous Sequencing of Paired Germline and Somatic Specimens Enhanced Clinical Care in Ovarian Cancer

In a small sample of women with ovarian cancer for whom simultaneous next-generation DNA sequencing was performed on paired germline and tumor specimens, test results influenced clinical decision-making for nearly 25% of patients. This study was presented at the Society of Gynecologic Oncology (SGO)’s 50th Annual Meeting on Women’s Cancer.

Targeted sequencing using the BROCA test, a gene panel designed for patients with a suspected hereditary cancer predisposition, was performed between July 2017 and July 2018 on paired peripheral blood (germline) and ovarian cancer tumor specimens (somatic) for 36 women with newly diagnosed ovarian cancer and 7 women with recurrent disease. Tumor specimens were obtained from surgical specimens, biopsy, or cytology in 72.1%, 25.6%, and 2.3% of cases, respectively.

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Chinese gene editing therapies are developing

China’s race to test ‘mutation-free’ gene-editing technology on cancer patients

BEIJING — China could be just over a year away from clinical trials of a new gene-editing therapy with an unprecedented high level of safety, according to a team of Chinese scientists involved in the research programme.

The scientists said the research, based on groundbreaking work published in the journal Science earlier this month, could help save the lives of many patients battling deadly diseases including cancer.

The existing genome-editing method works like a shotgun, breaking up a large numbers of genome strands and sometimes missing its intended target, causing unnecessary damage to cells.

The new tool under development in China targets and swaps individual “letters” in the DNA with extreme precision, avoiding cuts to the strands and significantly reducing the risk of unexpected mutations.

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Linking development and disease

Putting developmental diseases on the map

Most people use a map to understand the physical world around them. Now, genetic researchers have a map of their own to understand how developmental diseases work at the genetic level.  

In a recent study, UW graduate student Junyue Cao and Dr. Malte Spielmann from the Max Planck Institute profiled approximately 2 million cells from 61 mice embryos between 9 and 14 days old, resulting in a digital representation of how each cell type develops and its gene expression changes.

When a gene is between 9 and 14 days old, most cells that underlie major developmental diseases can be studied, according to Cao. With further application, Cao believes his study can be used as a reference to help other researchers understand how genetic diseases like autism, breast cancer, and parkinson’s disease develop in humans.

“If we can use this to comprehensively categorize the different cell states and their composition in disease or [the] aging process, then potentially, we can fully understand how they are generated in development and why there are different diseases and aging,” Cao said.

Cao and his team collected the largest single-cell dataset, Mouse Organogenesis Cell Atlas (MOCA), which consists of distinctions between individual cells. This dataset has recently been published and in this publication, the team created a genetic map of organ development.

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T-cell modification with CRISPR-Cpf1

Researchers engineer immune cells to fight cancer

Deep in the cells of the human immune system, DNA is constantly being replicated, transcribed and even mutated — but rarely does it change dramatically. Like every other living organism, humans and their genes developed from millions of years of evolutionary pruning.

But to Yale microbiologists, altering the entire genomes of T-cells — the body’s main offensive weapon against diseases such as cancer — is as simple as putting together a Lego set.

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Why don't we make heritable gene editing available to everybody?

We should not fear 'editing' embryos to enhance human intelligence, says leading geneticist George Church

One of the world’s leading geneticists says it will only be a matter of time before the genes of  human embryos are ‘edited’ to enhance their health and intelligence – and it is something we should embrace rather than fear.

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Next Next Gen Detection of Structural Variants

Accurate detection of complex structural variations using single-molecule sequencing

Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, and Michael C. Schatz

Nature Methods (Research article)

Abstract—Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.

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Introduction to organioids

What you need to know about organoids

By Chloe Reichel

Paola Arlotta, chair of and professor in the stem cell and regenerative biology department at Harvard University, is growing brain tissue in her lab. In recent years, scientists have developed new techniques that add another level to the two-dimensional tissue culture of yore (e.g., growing cells in a single layer in a petri dish). These cells grow and divide in three dimensions, ultimately giving rise to samples of tissue that resemble the organ itself. They’re called organoids, but many news headlines have described them as if they are real, live organs.

Take these headlines for example: “Scientists grow human brains in a dish” and “Scientists brew up the creepiest batches of brain balls yet.” While science is in its infancy, the headlines don’t reflect that, taking liberties in describing what organoids are and overstating their form and function.

“You imagine a mini brain in a dish — that’s not what these things are,” Arlotta stresses. That bears repeating: They’re not mini brains; they’re not brains in a dish. They’re brain organoids, simplified replicas with some of the features of the organ they model.

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The true number of human miRNAs

An estimate of the total number of true human miRNAs

Julia Alles, Tobias Fehlmann, Ulrike Fischer, Christina Backes, Valentina Galata, Marie Minet, Martin Hart, Masood Abu-Halima, Friedrich A Grässer,  Hans-Peter Lenhof, Andreas Keller, and Eckart Meese

Nucleic Acids Research (Research Article)

Abstract—While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.

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Connecting chromatin states (Epigenetics) to structural variation in human genomes

Chromatin organization modulates the origin of heritable structural variations in human genome 

Tanmoy Roychowdhury and Alexej Abyzov

Nucleic Acids Research (Article)

Abstract

“Structural variations (SVs) in the human genome originate from different mechanisms related to DNA repair, replication errors, and retrotransposition. Our analyses of 26 927 SVs from the 1000 Genomes Project revealed differential distributions and consequences of SVs of different origin, e.g. deletions from non-allelic homologous recombination (NAHR) are more prone to disrupt chromatin organization while processed pseudogenes can create accessible chromatin. Spontaneous double stranded breaks (DSBs) are the best predictor of enrichment of NAHR deletions in open chromatin. This evidence, along with strong physical interaction of NAHR breakpoints belonging to the same deletion suggests that majority of NAHR deletions are non-meiotic i.e. originate from errors during homology directed repair (HDR) of spontaneous DSBs. In turn, the origin of the spontaneous DSBs is associated with transcription factor binding in accessible chromatin revealing the vulnerability of functional, open chromatin. The chromatin itself is enriched with repeats, particularly fixed Alu elements that provide the homology required to maintain stability via HDR. Through co-localization of fixed Alus and NAHR deletions in open chromatin we hypothesize that old Alu expansion had a stabilizing role on the human genome.”

Cancers are tissue-specific, truly important perspective

Tissue-specificity in cancer: The rule, not the exception

Kevin M. Haigis, Karen Cichowski, and Stephen J. Elledge

Science (article)

“Abstract—We are in the midst of a renaissance in cancer genetics. Over the past several decades, candidate-based targeted sequencing efforts provided a steady stream of information on the genetic drivers for certain cancer types. However, with recent technological advances in DNA sequencing, this stream has become a torrent of unbiased genetic information revealing the frequencies and patterns of point mutations and copy number variations (CNVs) across the entire spectrum of cancers. One of the most important observations from this work is that genetic alterations in bona fide cancer drivers (those genes that, when mutated, promote tumorigenesis) show a remarkable spectrum of tissue specificity”

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Minimap2 makes sophisticated analysis possible on hand-held devices

The Garvan Institute brings DNA analysis capabilities to smartphones

The Garvan Institute of Medical Research has partnered with the University of NSW to take genome analysis ‘offline’ by adapting the algorithms that perform DNA analysis to require far less compute than current tools.

Medical practitioners fighting the Ebola and Zika viruses in New Guinea and Brazil have already used small genome sequencing devices that can clip on to a smartphone, but these devices still require high-performance computer workstations or reliable internet connections to identify genes.

Devices like the Oxford Nanopore Technologies MinION can create over a terabyte of data in 48 hours, but their use still isn’t commonplace because comparing or ‘aligning’ DNA from an unknown sample to a reference database to figure out what the sample is requires around 16 GB of RAM, which is beyond the capabilities of most mid-range laptops and flagship smartphones.

For cash-strapped medical programs in developing countries or during large-scale outbreaks, that kind of processing power isn’t easy to come by at scale, and a reliable internet connection can be just as hard to find.

In a new paper released in Nature, Garvan’s Genomic Technologies lead Dr Martin Smith and his team detailed the computational method for reducing the amount of memory needed for aligning sequences from 11GB to 2GB - well within the reach of mid-range smartphones.

The researchers adapted the Minimap2 program, which aligns DNA sequencing ‘reads’ to a reference library of known genomes.

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We'll need AI to deal with coming wave of genome data

Getting smart about artificial intelligence

By: Alison Cranage, Science writer

“Genomics is set to become the biggest source of data on the planet, overtaking the current leading heavyweights – astronomy, YouTube and Twitter. Genome sequencing currently produces a staggering 25 petabytes of digital information per year. A petabyte is 1015 bytes, or about 1,000 times the average storage on a personal computer. And there is no sign of a slowdown.”

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A boozy view of the human genome project, where it's been and might go

Human Genome Project: new alcohol abuse study could help us finally unlock secrets to beating genetic diseases

“Geneticists tried to exploit the revelations about the genome with studiesthat combed through thousands of tiny genetic changes in hundreds of thousands of patients with different diseases to see how they compared to healthy people. This enabled them to correlate genetic changes in diseased DNA in a manner unimaginable before June 2000. The “genetic architecture” of a wide number of conditions from cancers to schizophrenia to addiction became much better understood as a result.

Yet after the first few thousand studies were published, geneticists were horrified to discover that 98% of the disease-associated changes they’d identified in the genome do not occur in the genes. Instead, the vast majority of changes related to disease occur in the 98% of the genome that is not made up of genes – known as the “junk genome”, since few had the foggiest notion of what it was or how to study it.”

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Berkeley gets another CRISPR patent

University of California granted another CRISPR patent

UC Berkeley announced Tuesday it received a patent for a single-molecule guide RNA that can be used with the Cas-9 enzyme by the gene-editing tool CRISPR in plants, bacteria and mammalian cells.

Why it matters: Discovering new methods of making CRISPR's gene editing more precise are key to its future success in modifying crops and treating diseases. But, there's also a race among institutions — especially between UC and the Broad Institute — to own CRISPR patents that are potentially worth billions, per Reuters.

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Background: CRISPR can use different enzymes, most often Cas9, to target specific genes for editing, but there remain safety concerns, as it's been shown to sometimes cause unwanted deletions, edit the wrong genes or move genes around. Guide RNAs can be used to locate the proper DNA sequence that needs to be cut.

By the numbers: This is UC Berkeley's third CRISPR patent and they expect a fourth to be issued soon.

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or go even deeper: UC Berkeley team awarded second CRISPR-Cas9 patent

Lucence improving personalized liver cancer treatment with AI

Lucence Diagnostics to Develop AI Tools for Liver Cancer Treatment

Lucence Diagnostics, a genomic medicine company focused on personalizing cancer care, today announced a new project to develop AI algorithms for improving diagnosis and treatment of liver cancer. The goal is to combine the imaging and molecular data from liver cancer patients into smarter software tools that help physicians make better treatment decisions.

Lucence will be working with Olivier Gevaert, PhD, Assistant Professor of Medicine (Biomedical Informatics) and of Biomedical Data Science at the Stanford University School of Medicine. Having developed LiquidHALLMARK®, the world's first liquid biopsy next-generation sequencing test that analyzes the DNA of cancer-causing mutations and viruses, Lucence will contribute its genomics expertise and proprietary sequencing technology to this project.

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Coverage of the Genome-wide Off-target analysis by Two-cell embryo Injection

A Tool To Validate The Safety Of Gene Editing Systems

AsianScientist (Mar. 12, 2019) – A team of international scientists has developed a technique to evaluate the safety of genome-editing techniques. The research was published in Science. CRISPR-Cas9 is a new generation of gene-editing tool that has been widely used. However, the risk of off-target effects in vivo, which could lead to diseases such as cancer, remains a serious concern. A variety of off-target detection schemes have been developed, with most relying on the prediction of off-target sites based on sequence similarity or in vitro amplification. However, the latter process may introduce a large amount of noise, thus making it difficult to separate off-target signals from background noise. Whether CRISPR-Cas9 induces off-target effects has been controversial.

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Read the original article at Science