Zhang's group is moving beyond bulk
sequencing of tumor samples and is now conducting genomics on single cells.
Not exact matches
To determine how the cells switch from one type to another, they took three human uterine carcinosarcoma
samples and
sequenced the genomes
of cells in two parts
of each
tumor: the carcinoma and sarcoma components.
While the latter has a reputation for being hard to isolate, she explains that even degraded RNA generally contains enough intact
sequence to analyze — provided investigators can detect the scarce
tumor signals against the immense background
of other RNA molecules in a
sample.
A tissue slice, a
tumor biopsy, or a
sample of a bacterial culture yields a
sequence representing the average
of all
of the cells within it, even though researchers know there can be tremendous variation between those cells.
She has
sequenced hundreds
of tumor samples from across the island in an effort to understand how it evolves and how that affects the devils» survival rates.
The researchers analyzed the
samples using immunohistochemistry and RNA
sequencing to study the changes in the
tumor immune microenvironment
of patients who received and did not receive chemotherapy, and changes before and after chemotherapy.
The latter, presented by Eric Lander
of the Broad Institute in Cambridge, Massachusetts, would systematically
sequence tumor samples for mutations involved in cancer to speed up the search for new drugs and diagnostics.
A multicenter team
of researchers reports that a full genomic analysis
of tumor samples from a small number
of people who died
of pancreatic cancer suggests that chemical changes to DNA that do not affect the DNA
sequence itself yet control how it operates confer survival advantages on subsets
of pancreatic cancer cells.
NYGC computational biologists and members
of the Simon Laboratory at The Rockefeller University discussed the possibility
of using a series
of computer algorithms to search for
sequence differences between the
tumor samples and
samples of healthy liver tissue.
Information obtained via single - cell
sequencing from cells
sampled from each core indicate the likely location
of a cancerous
tumor (dotted lines encompassing cores 2, 3 and 6).
To search for other characteristics
of ccRCC
tumors that influences immunotherapy response or resistance, the researchers used whole - exome DNA
sequencing to analyze
tumor samples from 35 patients treated in a clinical trial with the checkpoint blocker nivolumab (Opdivo).
In the first cohort, researchers led by Jeeyun Lee, MD, from Sungkyunkwan University School
of Medicine in Seoul, performed whole exome
sequencing on
samples from paired synchronous primary and metastatic
tumors.
The researchers used an enhanced version
of a technique they developed called CAPP - Seq to isolate and
sequence circulating
tumor DNA, or ctDNA, from blood
samples from the patients.
A robotic device the size
of a dishwasher is humming nearby as dozens
of tiny tubes move
tumor samples through the
sequencing process.
Fifteen teams analyzed nearly 500 patients»
tumors for genetic aberrations and
sequenced the protein - coding DNA
of 316
samples — by far the largest cancer
sequencing effort to date.
More than 150 cancer researchers have divvied up the work
of sequencing about 500
tumor samples for each
of some 20 cancer types (10,000
samples in total) at a cost
of more than $ 375 million.
The idea is to
sequence 10,000
tumor samples for each
of several common cancers, such as breast and prostate.
First
of all, only the metastatic
sample was whole - genome
sequenced — the primary
tumor and matched normal were not.
Perhaps the most intriguing — and contentious — finding
of the paper (as highlighted by GT's In
Sequence magazine and Keith Robison on Omics Omics) was that few
of the somatic mutations in the metastasis were detected in the primary
tumor sample from 9 years earlier.
Another collaboration was unfolding among the cancer geneticists,
sequencing experts, clinical researchers, and surgical oncologists at Johns Hopkins, MD Anderson, and Baylor College
of Medicine to study 32 pairs
of head and neck
tumor and normal tissue
samples by whole - exome
sequencing and validate the findings in an additional 88
samples.
Grandis and Garraway decided to study a University
of Pittsburgh collection
of 74 pairs
of tumor and normal tissue
samples using the Broad's capacity to perform whole - exome
sequencing.
Scientists at the Beijing Institute
of Genomics rigorously
sampled nearly 300 regions from one slice
of the
tumor and
sequenced or genotyped each one looking for genetic changes.
By
sequencing the complete genomes
of primary
tumor, relapsed
tumor, and matched normal (skin)
samples from 8 AML patients, our group was able to study clonal evolution
of AML
tumors at the genetic level.
Targeted
sequencing was performed on available
tumor samples of 125 patients.
As part
of the Cancer Genome Atlas Project (TCGA), we've been applying both targeted (capture - based) and whole - genome
sequencing approaches to
tumor samples and matched normal controls.
Also, due to the high - priority
of say, validating somatic variants in a
tumor sample with 454
sequencing, we wanted something that could leverage faster aligners — parallelized BLAT for 454 and Bowtie for Illumina.
When the researchers
sequenced the
samples for genetic mutations and analyzed chromosome structure, they could trace the
tumors» evolutionary histories, much as evolutionary biologists trace the origins
of organisms back to their common ancestors based on fossils deposited in different geologic eras.
In the first set
of experiments, the Johns Hopkins scientists
sequenced nearly all protein - encoding genes in 10
of the 68
samples of pancreatic neuroendocrine
tumors and compared these
sequences with normal DNA from each patient to identify
tumor - specific changes or mutations.