Superior Performance of ThruPLEX®-FD Libraries in Whole Exome Enrichment with Agilent SureSelect® XT2 (149001)

Access to the newest DNA sequencing technologies in the past five years has offered a tremendous possibility
for understanding the fundamentals of genetic information. While the cost and the amount of data generated
are manageable for smaller genomes, the situation is more challenging for genomes of larger sizes. The
human genome exemplifies this problem since it contains over 3 billion base pairs. The biomedical
research community, who was among the first to adopt this technology as a tool to understand the cause of
disease, quickly concluded that the difficulty of their task could be reduced by focusing on the exome, that
portion of the genome that codes for over 20,000 proteins. This highly significant sub-section constitutes
only 1 – 2% of the human genome (30 Mbp), reducing both time and cost for sequencing and data analysis.

Tools to analyze the exome are now offered by several companies who have developed exome enrichment kits
for use with libraries prepared from a variety of human DNA sources including plasma, fresh frozen tissue, and
FFPE samples. These kits contain oligonucleotides designed to “capture” the genes of interest (in this case
the entire exome) by hybridization. These kits are provided by market leaders such as Agilent, Illumina and
Roche; other companies such as IDT provide custom panels that are used to capture a subset of genes.

While the vendors have excellent enrichment tools, the library preparation products offered to complement
these tools often fail to perform effectively with low sample amounts, a very common situation in many
fields of research. The Rubicon Genomics ThruPLEX®-FD Prep Kit is able to generate libraries with input DNA
amounts much lower than other kits while providing data of equal or better quality. In this note, we
demonstrate that libraries prepared from the ThruPLEX-FD Prep Kit are compatible with the Agilent
SureSelect®XT2 technology and provide superior whole exome enrichment performance when compared to
libraries prepared from the Agilent SureSelectXT2 Library Prep Kit.

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