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 …
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, …
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 …
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 …
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 …
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 …
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 …
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 …
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
Background Oncopanel genomic testing, which identifies important somatic variants, is
increasingly common in medical practice and especially in clinical trials. Currently, there is a …
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 …
exome sequencing data from 1ng of cancer cell line DNA. While traditional Whole Exome …