By Ellen Matloff
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Extra resources for Cancer Principles and Practice of Oncology: Handbook of Clinical Cancer Genetics
2 illustrates the differences in the number of SNPs used and their reported effects for the two largest DTC genomic profiling companies (23andMe2 and deCODE3) for some common cancers. 16,20 Both 23andMe and deCODE provide consumers with ongoing updates, (c) 2015 Wolters Kluwer. All Rights Reserved. Chapter 3 Direct-to-consumer Personal Genome Testing and Cancer Risk Prediction 39 Calculating a Consumer’s risk for cancer based on Four SNPs × × × × × × OR, odds ratio; RR, relative risk; SNP, single-nucleotide polymorphism; T/G/S/C, singlenucleotide bases.
With that in mind, you should expect a lot more data with WGS: Approximately, 120 Gb for a 30× WGS compared with approximately 5 to 10 Gb from WES. 6 However, because of the vastly smaller amount of genomic sequence, throughput and depth of coverage are frequently much greater with WES. In regard to clinical testing, there is not much difference in regard to cost with WES ranging from $4,000 to $15,000 and WGS from $7,500 to $10,000. (c) 2015 Wolters Kluwer. All Rights Reserved. 26 Principles and Practice of Oncology: Handbook of Clinical Cancer Genetics Current Limitations WGS/WES has both technical and clinical challenges.
1 In both WGS and WES, the DNA sample is first sheared randomly into small fragments, the length of which may vary based on the sequencing platform. Since the original sample contains multiple copies of genomic DNA, the random shearing results in the same segment of DNA being fragmented in different ways. This is important for the alignment step below. These fragments are then amplified through a polymerase chain reaction step similar to traditional sequencing. The result is a library containing hundreds of copies of each of the fragments.
Cancer Principles and Practice of Oncology: Handbook of Clinical Cancer Genetics by Ellen Matloff