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We characterized genome alterations in 1255 clinically annotated lung tumors of all histological subgroups to identify genetically defined and clinically relevant subtypes. More than 55% of all cases had at least one oncogenic genome alteration potentially amenable to specific therapeutic intervention, including several personalized treatment approaches that are already in clinical evaluation. Marked differences in the pattern of genomic alterations existed between and within histological subtypes, thus challenging the original histomorphological diagnosis. Immunohistochemical studies confirmed many of these reassigned subtypes. The reassignment eliminated almost all cases of large cell carcinomas, some of which had therapeutically relevant alterations. Prospective testing of our genomics-based diagnostic algorithm in 5145 lung cancer patients enabled a genome-based diagnosis in 3863 (75%) patients, confirmed the feasibility of rational reassignments of large cell lung cancer, and led to improvement in overall survival in patients with EGFR-mutant or ALK-rearranged cancers. Thus, our findings provide support for broad implementation of genome-based diagnosis of lung cancer.

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Abnormalities of the tumor-suppressor p53 gene have been discovered in human hepatocellular carcinoma (HCC). It is unclear, however, whether HCC related to chronic viral hepatitis is associated with p53 gene alterations. In this study, we have examined p53 abnormalities in HCC associated with hepatitis C and B virus (HCV and HBV) infections. Tissues from 18 HCC patients from several hospitals throughout the United States were collected (9 were HCV-infected, 5 were HBV-infected, 1 was HCV/HBV-infected, and 3 were non-virus-associated). Immunostaining with monoclonal pAb 1801 revealed expression of p53 protein in tumor-cell nuclei in one HCV-associated HCC, and in no case of HBV-associated HCC, while the nuclei of adjacent hepatocytes were negative. Using Hae III-digestion of chromosomal DNA, mutations at codon 249 were not found in any of 18 HCC tissues studied. Direct sequencing demonstrated a mutated codon 244 and a wild-type codon 249 in the conserved regions (exon 5-8) of p53 gene from the tumor tissue with nuclear p53 expression. By reverse-transcription-polymerase chain reaction (RT-PCR), the expression of p53 mRNA was demonstrated in tumor cells from 10 out of 16 HCC tissues. In conclusion, the specific mutation at codon 249 with G to T transversion was not observed in the HCCs associated with HCV or HBV infections. In HBV or non-virus-associated HCCs studied, no other p53 gene abnormalities were found. A point mutation at codon 244 with G to A transition of p53 gene was detected in only one of 10 HCV-associated HCCs, which suggests that p53 mutations may not play a significant role in HCV- or HBV-associated hepatocarcinogenesis.

We report a novel β+-thalassemia mutation found in a Vietnamese family. The molecular defect T→A lies at -72 of the β-globin gene promoter, within the conserved CCAAT box. The index case was a 5-year-old child having red blood cells indices close to normal and slightly increased level of HbA2 (3.96%). The expression of the mutated β allele was inferred by luciferase reporter assay in K562 cells. The β -72 determinant is the eighth β-thalassemic mutation identified in Vietnam and it was not previously reported in any population. The absence of homozygous or compound heterozygous states did not allow us to precisely predict either its clinical impact or its relevance in management programs. Our results further underline the importance of identifying and characterizing new or rare β+-thalassemic alleles in carrier screening and prenatal diagnosis.