Copy number variations in the human genome and strategies for analysis

On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA

Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.

Applications of array-CGH for lung cancer

This chapter summarizes the current knowledge on gene copy number changes found in lung tumors, and their application in the diagnosis, prognostication, and prediction of response to chemotherapy. Examples of the identification of specific "driver" oncogenes within amplified DNA segments are described. A model of how array-CGH could be integrated clinically into the routine workup of lung cancers in clinical laboratory is proposed.