Heinz Breu

Location:

36 east 41St Pl, San Mateo, CA 94403

Industry:

Biotechnology

Work:

Life Technologies
Senior Staff Engineer, Software
Hewlett-Packard 1982 - 1989
Member Technical Staff
Bell-Northern Research 1980 - 1982
Member of Scientific Staff

Education:

Skills:

Perl
R&D
Algorithms
Software Engineering
Software Development
Python
C++
Java
Genetics
Software Design
Life Sciences
C
Computational Biology
Bioinformatics

US Patent:

20020116135, Aug 22, 2002

Filed:

Jul 23, 2001

Appl. No.:

09/911903

Inventors:

Hugh Pasika - San Francisco CA, US
Yuandan Lou - Cupertino CA, US
David Holden - San Francisco CA, US
Heinz Breu - Palo Alto CA, US

International Classification:

G06F019/00
G01N033/48
G01N033/50

US Classification:

702/021000, 702/019000

Abstract:

Methods, systems, and articles of manufacture consistent with the present invention are provided for making allele calls. In certain embodiments, allele calling is accomplished by providing a committee machine that receives calls from several allele calling algorithms. By receiving calls from multiple allele calling algorithms, the committee machine makes calls containing a high level of confidence over a variety of conditions. Certain embodiments provide methods employing at least two algorithms and at least two quality values for allele calling. Unique individual algorithms for allele calling are also provided.

US Patent:

20030200032, Oct 23, 2003

Filed:

Mar 3, 2003

Appl. No.:

10/378694

Inventors:

Sean Keating - San Mateo CA, US
Heinz Breu - Palo Alto CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G01N033/48

US Classification:

702/019000

Abstract:

Peptide mass mapping is a technique whereby masses determined from mass spectrometry of a protein digest are compared to the masses of theoretical peptides derived from a reference protein, specified as an amino-acid sequence. In some cases differences between experimental and theoretical masses can be accounted for by chemical modifications of the actual protein with respect to the reference, often as a result of post-translational modification (PTM). Typically such modifications are applicable to specific sets of amino-acid residues. Analysis of these mass differences can therefore lead to identification of PTMs. In various cases, it is desirable that such analysis in general allow for the possibility of a peptide having several different PTMs, and furthermore it is desirable in various cases that the chemical compatibility of a putative combination of PTMs with the peptide sequence be verified. Embodiments are described herein wherein compatibility verification is formulated as a problem in graph theory. Theory and implementation of a solution are discussed and described.

US Patent:

20100129810, May 27, 2010

Filed:

Sep 8, 2009

Appl. No.:

12/555549

Inventors:

Douglas P. GREINER - Fremont CA, US
Carmen GJERSTAD - Millbrae CA, US
Janet S. ZIEGLE - Berkeley CA, US
Lee W. JONES - Hayward CA, US
Min-Yi SHEN - Mountain View CA, US
Heinz BREU - Palo Alto CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

C12Q 1/68

US Classification:

435 6

Abstract:

A system for performing quality control for nucleic acid sample sequencing is disclosed. The system has a set of solid supports, each support having attached thereto a plurality of nucleic acid sequences. The set has plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived. A method of preparing a quality control for performing nucleic acid sample sequencing and a method of validating a nucleic acid sequencing instrument are also disclosed.

US Patent:

20110257031, Oct 20, 2011

Filed:

Feb 11, 2011

Appl. No.:

13/026046

Inventors:

John BODEAU - San Mateo CA, US
Heinz BREU - Palo Alto CA, US
Kathleen PERRY - San Francisco CA, US
Adam HARRIS - Carlsbad CA, US
Patrick GILLES - Carlsbad CA, US
Miho Gilles - Carsbad CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

C40B 30/04
C07H 21/04
C40B 40/06

US Classification:

506 9, 506 16, 536 2431

Abstract:

Provided herein are systems, compositions and methods for tracking, sorting and/or identifying sample polynucleotides using nucleic acid barcodes. The barcodes provided herein are oligonucleotides that are designed to be uniquely identifiable. The nucleic acid barcodes have properties that permit them to be sequenced with high accuracy and/or reduced error rates. In some embodiments, the nucleic acid barcodes are designed to have certain nucleotide sequences that make up overlapping dibase color positions (also called color positions). The order of the overlapping dibase color positions can be determined using fluorophore-encoded dibase probes in a fluorophore color calling scheme to give high fidelity reads.

US Patent:

20110270532, Nov 3, 2011

Filed:

Apr 29, 2011

Appl. No.:

13/097328

Inventors:

Paolo VATTA - San Mateo CA, US
Onur Sakarya - Foster City CA, US
Heinz Breu - Palo Alto CA, US
Liviu Popescu - Sunnyvale CA, US
Asim Siddiqui - San Francisco CA, US
Fiona Hyland - San Mateo CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

G06F 19/00
G01N 33/48

US Classification:

702 20

Abstract:

Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

US Patent:

20110295514, Dec 1, 2011

Filed:

May 13, 2011

Appl. No.:

13/106998

Inventors:

Heinz Breu - Palo Alto CA, US
Danwei Guo - San Mateo CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

G06F 19/10

US Classification:

702 19

Abstract:

Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.

US Patent:

20130091126, Apr 11, 2013

Filed:

Oct 10, 2012

Appl. No.:

13/648998

Inventors:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA, US
Srikanth JANDHYALA - Foster City CA, US
Yuandan LOU - Cupertino CA, US
Asim SIDDIQUI - San Francisco CA, US
Mrunal AGATE - Pune, IN
Ameet DHAPULKAR - Pune, IN
Heinz BREU - Palo Alto CA, US
Amitabh SHUKLA - San Jose CA, US
Karl KUHLMANN - Menlo Park CA, US
Fiona HYLAND - San Mateo CA, US
Gulsah ALTUN - Foster City CA, US
Daryl THOMAS - Menlo Park CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

G06F 17/30

US Classification:

707722

Abstract:

Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

US Patent:

20130268207, Oct 10, 2013

Filed:

Mar 8, 2013

Appl. No.:

13/790713

Inventors:

Fiona HYLAND - San Mateo CA, US
Heinz BREU - Palo Alto CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

G06F 19/22

US Classification:

702 20

Abstract:

Systems and method for identifying somatic mutations can receive first ans second sequence information, determine if a variant present in the first sequencing information is also present in the second sequence information, and identify variants present in the first sequence information are somatic mutations when the variant is either not present in the second sequence information or the presence of the variant in the second sequence information is likely due to a sequencing error.