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Faster and cheaper mapping of DNA

onsdag 21 nov 18
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Rodolphe Marie
Lektor
DTU Nanotech
45 25 57 53

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Jonas Nyvold Pedersen
Lektor
DTU Nanotech
45 25 63 09

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Henrik Flyvbjerg
Lektor
DTU Nanotech
45 25 63 23

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Anders Kristensen
Professor
DTU Nanotech
45 25 63 31

Project acknowledgement

The results published in the PNAS paper were supported by the two projects Cell-O-Matic and PolyNano, both headed by Professor Anders Kristensen, DTU Nanotech.

Cell-O-Matic - European Union’s 7th Framework Programme grant 278204 www.cellomatic.eu

PolyNano - Danish Council for Strategic Research Grant 10-092322 www.polynano.org

New DTU Nanotech paper in PNAS.

A paper recently published in PNAS reports optical mapping of DNA from a single cell. Notably, it demonstrates isolation of a single cell, extraction of its DNA, and optical mapping of parts of this DNA, all achieved on an integrated micro- /nanofluidic device.

Optical mapping of DNA from cancer cells can point to large-scale structural variations within their genomes. This information can help to uncover genomic heterogeneity within a tumour, and maybe give an indication on how cells have developed in tissue and tumours. The researchers have worked with a team from the Oncology Department at Oxford University, lead by Professor Sir Walter F. Bodmer, and used a cancer cell line to demonstrate the method.

The device developed for the task is an injection-moulded low-cost plastic chip that can be mass-produced. The special feature of the polymer chip is its micro-fluidic design for integrated sample preparation, trapping and isolation of single cells, followed by extraction and optical mapping of their DNA.

PNAS Rodolphe Marie

Human cells are loaded on a single-use polymer chip. A single cell is captured, and its DNA is extracted and stained with a fluorescent dye. The DNA is then heated to create a ‘barcode’, i.e. a fluorescence pattern that depends on its specific DNA sequence. Individual DNA fragments are stretched, and their barcodes are imaged and analyzed. Comparison with a reference genome shows genetic changes in the specific cell.

Sequencing versus optical mapping

DNA sequencing methods have single-base-pair resolution, i.e. they identify, with some errors, every base pair in a DNA molecule. The drawback of sequencing is that its result is a sequence assembled from many so-called ‘reads’ that are only 100–150 base pair long, and the reads stem from many different copies of the DNA molecule.  Sequencing also requires complex sample preparation and a comprehensive data analysis afterwards.

Optical mapping techniques give a rough ‘finger-print’ of the underlying DNA sequence but do not have single-base-pair resolution. Their advantages are that optical mapping can work on individual molecules that are up to 1 million base pairs long. By comparison with a known reference genome, optical mapping can detect structural variations that are up to several 100-kilo base pairs long in DNA from a single cell. More importantly, with their paper, the authors demonstrate that the sample preparation can be done entirely on a lab-on-a-chip device, starting from a single cell and finishing with useful genomics data.

The authors emphasize the complementary nature of optical mapping and sequencing. Optical mapping provides only a coarse-grained picture of the underlying sequence but can give long-range structural information of individual cells. DNA sequencing, with its much higher resolution, can detect single base-pair-variations, but is challenged by long-range variations.

Towards a more efficient and personalized cancer treatment

Being able to map the genome at the single-cell level points towards a more efficient and personalized cancer treatment. Different types of cancer react differently to different types of treatments. So by looking at the cells in the tumour and their DNA, it is possible to learn what types of cells have developed, and hence to adapt the treatment accordingly towards a more efficient treatment of the specific patient.

Read the full paper here

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