Abstract: A first set of pixels forming a first set of rows and a first set of columns of a first image acquired by an image acquisition device is received. A first corrected set of pixels forming a first corrected set of rows and a first corrected set of columns is generated from the first set of pixels. Successive pixels of each row from the first corrected set of rows correspond to successive parallel lines in a plane defined by the sheet of light that are equally spaced along a first axis of a world coordinate system. Successive pixels of each column from the first corrected set of columns correspond to successive parallel lines in the plane defined by the sheet of light that are equally spaced along a second axis of the world coordinate system. Based on the first corrected set of pixels, a first set of points of the sheet of light is determined. The first set of points of the sheet of light is used to obtain a three-dimensional profile of the object.

Abstract: Acute myeloid leukemia (AML) has not benefited from innovative immunotherapies, mainly because of the lack of actionable immune targets. Novel tumor-specific antigens (TSAs) shared by a large proportion of AML cells are described herein. Most of the TSAs described herein derives from aberrantly expressed unmutated genomic sequences, such as intronic and intergenic sequences, which are not expressed in normal tissues. Nucleic acids, compositions, cells and vaccines derived from these TSAs are described. The use of the TSAs, nucleic acids, compositions, cells and vaccines for the treatment of leukemia such as AML is also described.

Abstract: T cells, notably CD8 T cells, are known to be essential players in tumor eradication as the presence of tumor-infiltrating lymphocytes (TILs) in several cancers positively correlates with a good prognosis. To eliminate tumor cells, CD8 T cells recognize tumor antigens, which are MHC I-associated peptides present at the surface of tumor cells, with no or very low expression on normal cells. Described herein a proteogenomic approach using RNA-sequencing data from cancer and normal-matched mTEChi samples in order to identify non-tolerogenic tumor-specific antigens derived from (i) coding and non-coding regions of the genome, (ii) non-synonymous single-base mutations or short insertion/deletions and more complex rearrangements as well as (iii) endogenous retroelements, which works regardless of the sample's mutational load or complexity.

Abstract: T cells, notably CD8 T cells, are known to be essential players in tumor eradication as the presence of tumor-infiltrating lymphocytes (TILS) in several cancers positively correlates with a good prognosis. To eliminate tumor cells, CD8 T cells recognize tumor antigens, which are MHC I-associated peptides present at the surface of tumor cells, with no or very low expression on normal cells. Described herein a proteogenomic approach using RNA-sequencing data from cancer and normal-matched mTEChi samples in order to identify non-tolerogenic tumor-specific antigens derived from (i) coding and non-coding regions of the genome, (ii) non-synonymous single-base mutations or short insertion/deletions and more complex rearrangements as well as (iii) endogenous retroelements, which works regardless of the sample's mutational load or complexity.

Abstract: Ovarian cancer, notably high-grade serous ovarian cancer (HGSC), the principal cause of death from gynecological malignancies in the world, has not significantly benefited from recent progress in cancer immunotherapy. While HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. Novel tumor-specific antigens (TSAs) shared by a large proportion of ovarian tumors are described herein. Most of the TSAs (>80%) described herein derives from aberrantly expressed unmutated genomic sequences, such as intronic and intergenic sequences, which are not expressed in normal tissues. Nucleic acids, compositions, cells and vaccines derived from these TSAs are described. The use of the TSAs, nucleic acids, compositions, cells and vaccines for the treatment of ovarian cancer is also described.

Abstract: A first set of pixels forming a first set of rows of a first image acquired by an image acquisition device is received. A first partially corrected set of pixels forming a first partially corrected set of rows is generated from the first set of pixels where successive pixels of a row from the first partially corrected set of rows correspond to successive parallel lines in a plane defined by the sheet of light that are equally spaced along a first axis of a world coordinate system. Based on the first partially corrected set of pixels and based on a peak extraction mechanism, a first partially corrected set of points of the sheet of light is extracted. The first partially corrected set of points is transformed to obtain a first corrected set of points of the sheet of light that are corrected in a first and a second direction.

Abstract: T cells, notably CD8 T cells, are known to be essential players in tumor eradication as the presence of tumor-infiltrating lymphocytes (TILS) in several cancers positively correlates with a good prognosis. To eliminate tumor cells, CD8 T cells recognize tumor antigens, which are MHC I-associated peptides present at the surface of tumor cells, with no or very low expression on normal cells. Described herein a proteogenomic approach using RNA-sequencing data from cancer and normal-matched mTEChi samples in order to identify non-tolerogenic tumor-specific antigens derived from (i) coding and non-coding regions of the genome, (ii) non-synonymous single-base mutations or short insertion/deletions and more complex rearrangements as well as (iii) endogenous retroelements, which works regardless of the sample's mutational load or complexity.

Abstract: Minor histocompatibility antigens (MiHAs) binding to certain human leukocyte antigen (HLA) alleles are described. These MiHAs were selected based on two features: (i) they are encoded by loci with a minor allele frequency (MAF) of at least 0.05; and (ii) they have adequate tissue distribution. Compositions, nucleic acids and cells related to these MiHAs are also described. The present application also discloses the use of these MiHAs, and related compositions, nucleic acids and cells, in applications related to cancer immunotherapy, for example for the treatment of hematologic cancers such as leukemia.

Abstract: Novel minor histocompatibility antigens (MiHAs) are described. These novel MiHAs were selected based on two features: (i) they are encoded by loci with a minor allele frequency (MAF) of at least 0.05; and (ii) they have adequate tissue distribution. Compositions, nucleic acids and cells related to these novel MiHAs are also described. The present application also discloses the use of these novel MiHAs, and related compositions, nucleic acids and cells, in applications related to cancer immunotherapy, for example for the treatment of hematologic cancers such as leukemia.

Abstract: Novel minor histocompatibility antigens (MiHAs) are described. These novel MiHAs were selected based on two features: (i) they are encoded by loci with a minor allele frequency (MAF) of at least 0.05; and (ii) they have adequate tissue distribution. Compositions, nucleic acids and cells related to these novel MiHAs are also described. The present application also discloses the use of these novel MiHAs, and related compositions, nucleic acids and cells, in applications related to cancer immunotherapy, for example for the treatment of hematologic cancers such as leukemia.

Abstract: A novel method for human minor histocompatibility antigen (MiHA) discovery, novel MiHAs identified using this method, as well as uses of the novel MiHAs, are described. One of the features of the novel method is the inclusion of personalized translated transcriptome and/or exome in the database used for peptide identification by mass spectroscopy (MS). Candidate MiHAs are identified by comparing the personalized transcriptome and/or exome to a reference genome and/or to the transcriptome and/or exome of an HLA-matched subject.

Abstract: Novel minor histocompatibility antigens (MiHAs) are described. These novel MiHAs were selected based on two features: (i) they are encoded by loci with a minor allele frequency (MAF) of at least 0.05; and (ii) they have adequate tissue distribution. Compositions, nucleic acids and cells related to these novel MiHAs are also described. The present application also discloses the use of these novel MiHAs, and related compositions, nucleic acids and cells, in applications related to cancer immunotherapy, for example for the treatment of hematologic cancers such as leukemia.

Abstract: Genes exhibiting specific mutational and/or transcriptional patterns in poor prognosis AMLs, such as EVI1-rearranged acute myeloid leukemias (EVI1-r AMLs), relative to other types of AMLs and/or normal CD34+ cells, are disclosed. The use of these mutational and/or transcriptional patterns, for example the expression level of the PRKC Apoptosis WT1 Regulator (PAWR) gene, for the diagnosis or prognosis of AMLs, including intermediate-risk AMLs, is also disclosed.

Abstract: A method for recognizing an occurrence of an object in an image is provided where the appearance of the object may vary from one occurrence to another. The method includes defining a model set for object recognition, the model set including at least one model, acquiring a target image, processing the target image according to a set of morphological operations to obtain a set of morphologically-processed target images, performing object recognition on the set of morphologically-processed target images for the defined model set, and selecting at least one candidate occurrence of a model of the defined model set in the target image based on the object recognition performed on the set of morphologically-processed target images.

Abstract: A novel method for human minor histocompatibility antigen (MiHA) discovery, novel MiHAs identified using this method, as well as uses of the novel MiHAs, are described. One of the features of the novel method is the inclusion of personalized translated transcriptome and/or exome in the database used for peptide identification by mass spectroscopy (MS). Candidate MiHAs are identified by comparing the personalized transcriptome and/or exome to a reference genome and/or to the transcriptome and/or exome of an HLA-matched subject.

Abstract: A novel method for human minor histocompatibility antigen (MiHA) discovery, novel MiHAs identified using this method, as well as uses of the novel MiHAs, are described. One of the features of the novel method is the inclusion of personalized translated transcriptome and/or exome in the database used for peptide identification by mass spectroscopy (MS). Candidate MiHAs are identified by comparing the personalized transcriptome and/or exome to a reference genome and/or to the transcriptome and/or exome of an HLA-matched subject.

Abstract: A novel method for human minor histocompatibility antigen (MiHA) discovery, novel MiHAs identified using this method, as well as uses of the novel MiHAs, are described. One of the features of the novel method is the inclusion of personalized translated transcriptome and/or exome in the database used for peptide identification by mass spectroscopy (MS). Candidate MiHAs are identified by comparing the personalized transcriptome and/or exome to a reference genome and/or to the transcriptome and/or exome of an HLA-matched subject.

Abstract: The present invention provides nucleotide sequences, methods and compositions that enable the experimental determination as to whether any gene in the genome of Aspegillus fumigatus is essential, and whether that gene is required for virulence or pathogenicity. The methods involve the construction of genetic mutants in which a target gene is placed under conditional expression. The identification of essential genes and those genes critical to the development of virulent infections, provides a basis for the development of screens for new drugs against Aspergillus fumigatus.