Next-generation sequencing of newborn screening genes: the accuracy of short-read mapping.

Newborn screening programs are an integral part of public health systems aiming to save lives and improve the quality of life for infants with treatable disorders. Technological advancements have driven the expansion of newborn screening programs in the last two decades and the development of fast, accurate next-generation sequencing technology has opened the door to a range of possibilities in the field. However, technological challenges with short-read next-generation sequencing technologies remain significant in highly homologous genomic regions such as pseudogenes or paralogous genes and need to be considered when implemented in screening programs. Here, we simulate 50 genomes from populations around the world to test the extent to which high homology regions affect short-read mapping of genes related to newborn screening disorders and the impact of differential read lengths and ethnic backgrounds. We examine a 158 gene screening panel directly relevant to newborn screening and identify gene regions where read mapping is affected by homologous genomic regions at different read lengths. We also determine that the patient's ethnic background does not have a widespread impact on mapping accuracy or coverage. Additionally, we identify newborn screening genes where alternative forms of sequencing or variant calling pipelines should be considered and demonstrate that alterations to standard variant calling can retrieve some formerly uncalled variants.

A modified matrix perfusion-microcarrier bead cell culture system. I. Adaptation of the matrix perfusion system for growth of human foreskin fibroblasts.

Two strains of human foreskin fibroblast cells were incapable of sustained growth in a matrix perfusion culture system, possibly because of their inability to attach to the fiber surfaces. Addition of microcarrier beads to the extracapillary space allowed attaining high cell densities in excess of 10(7) cells per culture unit. Microcarrier beads were tested in hollow fiber culture devices containing membranes of 10(4) or 10(5) D nominal porosities. Best results were obtained when initial cell densities of at least (2-3) x 10(6) cells were used in units with 10(5) D pore size membranes and DEAE-Sephadex or polyacryl-amide microcarrier beads in the extracapillary space. This extension of the matrix perfusion system should be useful for growing other anchorage dependent cells while retaining the advantages of perfusion culture.

A modified matrix perfusion-microcarrier bead cell culture system. II. Production of human (beta) interferon in a matrix perfusion system.

Addition of microcarrier beads to a matrix perfusion cell culture system allowed growth of anchorage dependent human foreskin fibroblasts which would not grow in the culture units alone. The utility of the system for collection of cellular products was demonstrated by the induction and harvesting of human (beta) interferon. Interferon production was highest in perfusion cultures when medium was circulated throughout the induction and when inducer containing 100 mug/mL polyriboinosinic: polyribocytidylic acid was placed directly in contact with cells in the extracapillary space. These conditions provided 4-to-10-fold greater interferon yields per cell, and approximately 12-fold increases per vessel, than monolayer cultures. Perfusion grown cells produced interferon at a maximal level for 20 h postinduction compared to approximately 2 h for monolayer grown cells, thus giving a higher total yield of interferon. Other procedures increasing the efficiency of the system included priming with 50 U/mL interferon standard, reinduction of cells, use of antibiotic free medium, reduced serum concentrations, and in vitro aging of the cells.