The required service is extension to metagenome sequencing that took place in 2021 by MGI Tech Latvia on >5000 gut microbiota samples from the Health and Early Life (HELMI) birth cohort NCT03996304. In total, we have collected approx. 10,000 stool samples from infants and their parents in the HELMI cohort. Now we want to extend the previously sequenced dataset by sequencing additional, earlier timepoints (3 and 6 week old infant stool samples) from the same study subjects.
Since these new samples are from the same subjects, it is necessary to use the same, i.e. MGI, sequencing technology for the sake of data comparability. It is not possible to obtain comparable sequencing data with other sequencing technologies.
The required service consists of shotgun metagenome sequencing of stool DNA samples extracted from 3 and 6 week old infants. Samples are already pipetted to plates according to MGI metagenome sequencing guidelines; we have in total 1969 samples in 21 plates that each have empty wells on positions 2D and 8D (42 in total), and in addition 5 bridging samples from the 2021 sequenced bacth, summing up to 1974 samples to pay.
The samples to be sequenced are collected from newborns and they have for biological reason low DNA content and additionally have somewhat variable qualities as specified below. Hence, we want to apply a customised two stage pricing, which consists of 1) library prep and quality control for all samples, and 2) sequencing of libraries that pass the QC. Because the number of samples passing to stage 2 can be only estimated, the total value of the procurement is also an estimate.