The Scripps Research Institute

Northwestern University

Roche Molecular Systems, Inc.

Jumpcode Genomics, Inc.

Daniel R Salomon

Steven Robert Head

Sunil M Kurian

Phillip T Ordoukhanian

Michael Abecassis

John J Friedewald

Steve Head

Josh Levitsky

Nancy J Schoenbrunner

Henry A Erlich

Keith Brown

Alison Tsan

Cherie Holcomb

Nick Newton

Bryan Hoglund

Azeem Siddique

Priscilla Moonsamy

Melinda Rastrou

Donald V Cramer

By a genome-wide gene analysis of expression profiles of over 50,000 known or putative gene sequences in peripheral blood, the present inventors have identified a consensus set of gene expression-based molecular biomarkers associated with chronic allograft nephropathy and/or interstitial fibrosis and tubular atrophy CAN/IFTA and subtypes thereof. These genes sets are useful for diagnosis, prognosis, monitoring and/or subtyping of CAN/IFTA.

Gene expression profiles associated with chronic allograft nephropathy

By a genome-wide gene analysis of expression profiles of over 50,000 known or putative gene sequences in peripheral blood, the present inventors have identified a consensus set of gene expression-based molecular biomarkers associated with subclinical acute rejection (subAR). These genes sets are useful for diagnosis, prognosis, monitoring of subAR.

Gene expression profiles associated with sub-clinical kidney transplant rejection

The present disclosure provides methods, compositions, and kits for methods that can improve techniques nucleic acid analysis, and can allow for more reliable and accurate targeted, multiplexed, high throughput sequencing. The methods, compositions, and kits can be used for sequencing target loci of nucleic acid. The methods, compositions, and kits disclosed herein can be used for assisted de novo targeted sequencing. The methods, compositions, and kits disclosed herein can also be used for library labeling for de novo sequencing and phasing.

Methods of sample preparation

By a genome-wide gene analysis of expression profiles of known or putative gene sequences in peripheral blood and biopsy samples, the present inventors have identified a consensus set of gene expression-based molecular biomarkers for distinguishing liver transplantation patients who have Acute Rejection (AR), Hepatitis C Virus Recurrence (HCV-R), both AR/HCV-R, or Acute Dysfunction No Rejection (ADNR). These molecular biomarkers are useful for diagnosis, prognosis and monitoring of liver transplantation patients.

Molecular signatures for distinguishing liver transplant rejections or injuries

Methods, compositions and kits are provided herein for insertional modification of nucleic acids by, for example transposase-mediated covalent insertion of insertion sequence into a sample nucleic acid molecule. Using sequence of the insertion to direct amplification of adjacent nucleic acid sequence, and using bar codes to map amplified sequence to partitions, one can map sample nucleic acid sequence to single molecules of the nucleic acid sample that are derived directly from the sample nucleic acid molecule.

Methods and compositions for sequencing

Disclosed herein are methods of detecting, predicting or monitoring a status or outcome of a transplant in a transplant recipient.

Methods and systems for analysis of organ transplantation

The invention is a method of detecting or assessing solid organ graft (transplant) rejection by detecting donor-specific HLA alleles in a blood sample of a graft (transplant) recipient. The invention further comprises a method of detecting the presence of maternal cells in a blood sample of an offspring.

Non-invasive early detection of solid organ transplant rejection by quantitative analysis of mixtures by deep sequencing of HLA gene amplicons using next generation systems

The invention provides a composition and a method for preventing or ameliorating the causes of chronic allograft rejection of a donor organ by a transplant recipient. The method includes concomitant administration to the allograft recipient of therapeutically effective amounts of cyclosporin and 2-chlorodeoxyadenosine. The composition comprises a combination of these two immunosuppressive drugs in therapeutically effective amounts suitable for the practice of the method.

Growing community of inventors

La Jolla, CA, United States of America

Daniel R Salomon