Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

…, S Greer, JY Lee, K Belhocine, KM Giorda… - Nature …, 2016 - nature.com
Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of
genetic variation. We present a microfluidics-based, linked-read sequencing technology that …

[HTML][HTML] Extensive sequencing of seven human genomes to characterize benchmark reference materials

…, M Schnall-Levin, HS Ordonez, PA Mudivarti, K Giorda… - Scientific data, 2016 - nature.com
… The Proteinase K and RNaseA digestion was incubated for 30 min at 25 C. Genomic DNA
was purified using MagAttract Suspension G with Buffer MB, washed twice with Buffer MW1, …

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

…, AK Eterovic, L Feng, A Ghosal, K Giorda… - Nature …, 2021 - nature.com
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology,
but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here …

Health and population effects of rare gene knockouts in adult humans with related parents

…, AH Barnett, C Bates, S Bellary, NA Bockett, K Giorda… - Science, 2016 - science.org
Examining complete gene knockouts within a viable organism can inform on gene function.
We sequenced the exomes of 3222 British adults of Pakistani heritage with high parental …

A hybrid approach for de novo human genome sequence assembly and phasing

…, C Lin, Ž Džakula, H Cao, SA Schlebusch, K Giorda… - Nature …, 2016 - nature.com
… Second, Linked-Reads are produced by random k-mer amplification of the 50- to 100-kb
molecules present in the small partitions. As such, there are times when these molecules are …

[HTML][HTML] Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel …

…, HA Coleman, MK Slevin, K Giorda, M Light, K Lai… - BMC genomics, 2018 - Springer
Background Sample index cross-talk can result in false positive calls when massively parallel
sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant …

Viroporins customize host cells for efficient viral propagation

KM Giorda, DN Hebert - DNA and cell biology, 2013 - liebertpub.com
… Strebel K.The envelope glycoprotein of human immunodeficiency virus type 2 enhances …
Kirkegaard K.Remodeling the endoplasmic reticulum by poliovirus infection and by individual …

[HTML][HTML] TMTC1 and TMTC2 are novel endoplasmic reticulum tetratricopeptide repeat-containing adapter proteins involved in calcium homeostasis

JC Sunryd, B Cheon, JB Graham, KM Giorda… - Journal of Biological …, 2014 - ASBMB
The endoplasmic reticulum (ER) is organized in part by adapter proteins that nucleate the
formation of large protein complexes. Tetratricopeptide repeats (TPR) are well studied protein …

[HTML][HTML] A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

…, J Foox, M Francescatto, Y Fu, C Furlanello, K Giorda… - Genome biology, 2021 - Springer
Background Oncopanel genomic testing, which identifies important somatic variants, is
increasingly common in medical practice and especially in clinical trials. Currently, there is a …

Using 1ng of DNA to detect haplotype phasing and gene fusions from whole exome sequencing of cancer cell lines

…, P Mudivarti, K Giorda - Cancer Research, 2015 - AACR
We have used a new platform from 10X Genomics to obtain ultra-deep and long-range
exome sequencing data from 1ng of cancer cell line DNA. While traditional Whole Exome …